Most insects that feed on green plants are specialists, meaning that they feed on just a narrow range of plant species. This reduces competition, especially if the host plant contains chemical deterrents that are toxic to other insects. But specialists cannot easily switch to feed on other plants, making them vulnerable to changes in the availability of the particular food type that they eat.

Generalist insects, on the other hand, are able to consume a wide range of diets. This makes them more robust to changes in food availability, but it is unclear how these insects deal with the wider range of chemical compositions of their food. Do they convert food into energy using the same chemical process, or metabolism, for all the different things they eat? Or do generalists have a specific metabolic pathway for each food type?

To answer this question, Olazcuaga, Baltenweck et al. studied the metabolism of a generalist fruit fly species. The team compared four types of fruit (blackcurrant, cherry, cranberry and strawberry) and isolated separate groups of flies so that they each ate only one type of fruit. By comparing the chemical composition of the flies with that of the fruit they ate, they were able to work out how each fruit type was metabolised. They found that the flies converted food into energy using the same process regardless of the type of fruit they ate. This lack of a specialist metabolic pathway for each fruit type meant that some chemicals were not metabolised and accumulated in the fly’s body instead. This build-up of unprocessed chemicals is likely to be harmful to the fly.

The results of Olazcuaga, Baltenweck et al. suggest that generalist insects do not actively adapt their metabolism to new food types. It’s more likely that they try different types of food as the opportunity arises, regardless of the fact that some of the food will not be converted into energy and may harm them long term. These findings are important because they give us an insight into how the chemistry of a plant can shape the physiology of the organisms that consume it, and vice-versa. These insights are a crucial step in developing sustainable agriculture practices that must consider tackle how plants are pollinated, how plant seeds are dispersed and what type of pest control to use.

One of the most salient features of living organisms is their diversity in terms of ecological requirements. Some species show extreme specialization in their environment (e.g. obligate symbionts), while others are able to use a wide range of resources and tolerate many environmental conditions. Furthermore, these relationships between organisms and their biotic and abiotic environments are dynamic at various spatial and temporal scales. As such, the concepts of niche breadth and ecological specialization are of paramount importance in ecology and evolutionary biology (Futuyma and Moreno, 1988; Sexton et al., 2017).

The dietary requirements of phytophagous insects are a textbook example of variance in niche breadth (Forister et al., 2012; Futuyma and Moreno, 1988; Jaenike, 1990). In this group, the vast majority of species are specialists of one family of plants (Forister et al., 2015) and this specialization is often accompanied by extreme morphological and/or physiological specializations to exploit a particular plant (e.g. Berenbaum, 1981; Hotti and Rischer, 2017). In contrast, some rarer species display a much wider niche breadth, allowing them to consume up to several dozen plant families (Clarke et al., 2005; Forister et al., 2015). The larger proportion of specialists than generalist species (Forister et al., 2015), as well as the fact that transitions between specialism and generalism, are bidirectional (Day et al., 2016; Janz et al., 2001; Nosil, 2002; Nylin et al., 2014), raises questions about the origin and maintenance of generalism (Forister et al., 2012; Singer, 2008), and its biochemical basis.

From a physiological point of view, dietary generalism has been much less experimentally studied than specialism, probably in part because it requires the simultaneous consideration of numerous host species and the tracking of physiological responses that may involve far more components than specialism. Additionally, the study of dietary generalism lacks the intellectual appeal of bi-species interactions leading to biochemical and genetic arm-races. Indeed, many research scrutinized the evolution of plant defenses and their corresponding detoxifying pathways in herbivores (e.g. the glucosinolate–myrosinase system of Brassicaceae countered by Spodoptera frugiperda; Winde and Wittstock, 2011). Comparatively, knowledge about how generalist species cope with a wide variety of plant biochemistry is scarce (but see Roy et al., 2016).

The core question of dietary generalism at the level of the organism is how a generalist species metabolizes different diets, which involves some basic issues that are still pending. For instance, do individuals of a generalist species have a unique biochemical response to all diets or do they differ according to their diet? In evolutionary terms, do dietary generalist species exhibit a canalized response to different dietary environments through a single, neutral, and generic use of hosts (H1; hereafter termed ‘metabolic generalism’), or do they show multiple specialized, adapted uses of different hosts (H2; hereafter termed ‘multi-host metabolic specialism’)? Broad organismal-level patterns of biochemical composition can help answer this question because individuals on different diets should be chemically similar across diets according to the former hypothesis, or mostly dissimilar according to the latter (Figure 1).

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To refine our understanding of diet generalism, we here use an untargeted metabolomics approach to characterize the metabolic impact of various fruit-based diets on the generalist insect species Drosophila suzukii (Figure 1A). The range of molecular compounds detected and quantified by current metabolomic methods may span many hundreds or thousands of molecules, ensuring a high-quality snapshot of the individuals’ physiological state (Johnson et al., 2016). Additionally, untargeted metabolomics provides the opportunity to directly compare diets and individuals that consume them, in an objective and repeatable way. The invasive Drosophila suzukii (the spotted wing Drosophila) displays an exceptional diet breadth of over 20 plant families (Asplen et al., 2015; Bellamy et al., 2013; Cini et al., 2014; Kanzawa, 1939; Kenis et al., 2016; Lee et al., 2011; Lee et al., 2015; Poyet et al., 2015). While multiple experimental studies have found that different diets have an influence on its larval development (Kenis et al., 2016; Olazcuaga et al., 2019; Poyet et al., 2015), it is widely accepted that D. suzukii is a diet generalist species.

By directly comparing the metabolomes of fruits and flies that consume them, we investigated the following question: Do generalist individuals have a single physiological response to various diets (‘metabolic generalism’) or do they exhibit specific responses to these various diets (‘multi-host metabolic specialism’)? We first verified how biochemically different were the selected major host plant species used by D. suzukii. Then, we examined whether generalist individuals use different host plants in a similar way, qualitatively and quantitatively. Finally, we attempted to discriminate individuals of a generalist species according to their diet and identify diet-specific metabolites in generalist individuals.

The metabolomes of four major crop fruits (blackcurrant, cherry, cranberry, and strawberry) and their corresponding flies (that consumed them both at the larval and early adult stages) were characterized simultaneously using ultra-high-performance liquid chromatography coupled to mass spectrometry (UHPLC-MS; Figure 1A). Our untargeted approach enabled the detection and relative quantification of a set of 11,470 unique ions that were found in at least one fruit or fly sample. While the simultaneous processing of fruit and flies’ samples provided a single integral dataset enabling direct comparison between diets and consumers, some analyses required the fruit-related and fly-related data to be separated, resulting in a fruit dataset and a fly dataset. Although the integral, fruit, and fly datasets are based on ions characterized by UHPLC-MS, some ions will be referred to as ‘compounds’ or ‘metabolites’ later in the manuscript, depending on the context. Importantly, we took care to standardize the fly and integral dataset using control flies (i.e. flies that developed on an artificial diet only) to avoid including ions derived from the artificial component of our fruit diets (see Methods section for more details). Controlled and raw fly datasets yielded similar results (see Appendix 1). We here present the results of the analyses of the controlled fly dataset.

Host use

Whether individuals of a generalist species process all types of diet in a similar, generic way (‘metabolic generalism’) or show specific pathways to metabolize unique compounds of different diets (‘multi-host metabolic specialism’) entails largely non-overlapping expectations for the both qualitative and quantitative biochemical composition of individuals relatively to their diets (Figure 1).

The first approach is based on the fact that metabolic generalism is expected to result in particular patterns of overlap between ions when all fruits and flies are considered together (Figure 1B). If D. suzukii is a metabolic generalist, flies should all share a large part of their ions, fly ions specific to a particular diet should be rare or absent, and/or ions specific to single fruit-fly pair (i.e. a pair of fruit and flies grown over the same fruit) should also be rare (Figure 1C, left panel). On the contrary, multi-host metabolic specialism would be detected by any given fruit-fly pair sharing large amounts of ions but not with other pairs, and/or large amounts of ions found only in flies that are specific to each diet (Figure 1C, right panel). To test these predictions, we computed intersection sizes between all fruits’ and flies’ ions from a presence/absence (qualitative) dataset derived from our quantitative integral dataset. Comparison of the overall intersections of ions present in the different fruits and the flies grown over these fruits showed that most ions are shared between large groups of fruits and flies (i.e. with higher degrees of intersection; Figure 2A). The largest intersection includes 3691 ions shared by all fruits and all flies (32%). The second largest intersection comprises 1103 ions shared among all flies (and absent in fruits; 10%). The fourth largest intersection contains 412 ions shared among all fruits (and no flies; 4%). High-order degree characterizes all other largest intersections, except for a set of 283 ions uniquely found in blackcurrant fruits. Figure 2B focuses on the sets of ions found uniquely in fruits, flies, or fruit-fly pairs (i.e. the intersections of degree 1 and 2). While ions found uniquely in each fruit are not uncommon (>100 ions for all fruits), ions found uniquely in flies raised on a particular diet are rare (two in cherry-fed flies, seven in cranberry-fed flies, and none in strawberry-fed and blackcurrant-fed flies). Ions that are distinctive of a particular fruit-fly pair are also seldom, ranging from 69 in the blackcurrant fruit-fly pair to only seven in the strawberry fruit-fly pair.

Figure 2

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Similarity and dissimilarity in the use of different host plants could stem from the metabolic fate of common and unique fruit metabolites when ingested by flies. Differently-fed flies metabolizing compounds that are shared between fruits to produce metabolites shared between flies would be indicative of ‘metabolic generalism’ (Figure 1D). On the opposite, differently-fed flies metabolizing compounds private to a given fruit to produce new metabolites (mostly not shared between flies) would be indicative of ‘multi-host metabolic specialism.’ We thus inspected the intersection degrees of all fruits and the intersection degrees of all flies, together with their relationships (Figure 3). First, the intersection of all fruits (left column) is largely formed from ions common to all fruits (48.6% of all ions present in fruits). Ions present in lower degree intersections are found in approximately equal proportions to each other (intersections of degree 3, 2, and 1 represent 20.1%, 14.8%, and 16.5% respectively). Approximately 10% of all ions found in this study are not detected in fruits, but only in flies (yellow stack, left column). Second, the intersection degrees of flies show marked differences from those of the fruits (Figure 3, right column). These include a higher proportion of metabolites common to all flies (76.3% of all ions present in flies), smaller proportions of lower degree intersections (intersections of degrees 3, 2, and 1 represent 10.6%, 4%, and 9% of all ions present in flies, respectively), and a large proportion of fruit metabolites that are absent in flies (19.5% of all detected ions). Third, the inspection of the relationships between fruit and flies’ metabolomes shows that most common fruit ions are the largest, but not unique, part of the most common fly ions. It is important to note that 92% of ions that were present in flies but not in any fruit (i.e. derived from de novo produced metabolites; yellow stack, left column) are ions common to all flies regardless of their diet (Figure 3, yellow flow from 0 to 4). In contrast to the most common fruit ions, ions unique to a single fruit or shared by a few fruits (fruit intersection degrees 1–3) follow roughly the same distribution of 1/3 being shared by all flies, 1/3 being shared by a few flies, and 1/3 being shared by no flies. This includes ions unique to a given fruit, 39.4% of which are found in all flies. Fly ions that are specific to a given diet come from fruit ions with various intersection degrees. In particular, 27.1% are common to all fruits, 21.5% are unique to a single fruit and only 1.1% are produced de novo (nine ions).

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Finally, we visually investigated the multi-dimensional clustering of fruits’ and flies’ metabolomes using a PCA using the integral dataset (Figure 1F). If diets are the main influence on flies’ metabolomes, flies should not cluster together and rather localize close to their corresponding fruit, especially on the second dimension (Figure 1G, right panel). On the contrary, if flies similarly process different diets, flies’ metabolomes should cluster together, away from the fruits (Figure 1G, left panel). Results of the PCA show that while different fruits are easily discriminated, differently-fed flies all clustered into a single group (Figure 3—figure supplement 1).

Altogether, our analyses underscore that the metabolomes of flies fed on different fruits are mostly identical, especially from a qualitative standpoint, and unanimously point to metabolic generalism, over multi-host metabolic specialism, as a mechanism promoting diet breadth.

Metabolomic discrimination of diets in flies

Given the overall qualitative similarity of flies that developed on different diets, we then investigated whether quantitative hallmarks of diet consumption could be detected in flies. A PCA focusing on the fly dataset demonstrated that flies’ diets can be readily inferred (Figure 4). While the first dimension of the PCA (20% of variance explained) discriminates between biological replicates of our experiment (i.e. generations of flies), the second and third dimensions of the PCA (18.3% and 10.5% of variance explained, respectively) discriminate fly metabolomes according to their diet.

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To further detect which ions were indicative of the development of particular fruits, we then computed diet-specific binomial linear models with Elastic Net regularization. We specifically aimed at producing two lists of diet-specific ions based on their quantitative levels in flies’ metabolomes and on two sets of parameters designed (i) to optimally classify flies according to their diet (‘large’ list) and (ii) to be as short as possible to allow manual curation of the identified ions (‘compact’ list, see Materials & methods for details). This statistical approach yielded a ‘large’ list consisting of 169 fly ions associated with a blackcurrant diet, 103 with a cherry diet, 121 with a cranberry diet, and 40 with a strawberry diet. All four ‘large’ models enabled a perfect classification of flies according to their diet (ratio of deviance explained >98%). As expected, these ions are part of the top set of ions driving the explained variance in the dimensions of the previous PCA, as shown by their location in the ion space (Figure 4—figure supplement 1). The ‘compact’ set of Elastic Net parameters attained a similar deviance ratio and yielded a list of 62 fly ions associated with a blackcurrant diet, 40 with a cherry diet, 49 with a cranberry diet, and 15 with a strawberry diet. All fly ions in the ‘compact’ list were present in the ‘large’ list. As shown in Figure 4—figure supplement 2, the ‘large’ list of fly ions can perfectly class fly samples according to their diet. It also suggests that most of these fly ions are present in similar quantities in their respective fruit, with few exceptions. Consistent with these results, we verified that ions of the ‘large’ list for a given flies’ diet were significantly more present in flies of the said diet than in flies developed on other diets and also more present in the said fruit than on other fruits (Figure 4—figure supplement 3). Depending on the diet, quantities of these distinctive ions found in flies could be correlated to the quantity found in the fruit (e.g. blackcurrant; Figure 4—figure supplement 4A, B) or not (e.g. cherry, cranberry, strawberry; Figure 4—figure supplement 4C, D).

Diet-associated ions were found to be part of intersections of every degree, both in flies and in fruits (Figure 4—figure supplement 5). In flies, large parts of these ions were specific to the flies that consumed the diet, especially for blackcurrant-fed flies (degree 1: 76%, 31%, 33%, and 25% in blackcurrant, cherry, cranberry, and strawberry-fed flies, respectively). However, ions contained in intersections of larger degrees were also observed, including ions found in all flies (degree 4: 16%, 48%, 31%, and 53% in blackcurrant, cherry, cranberry, and strawberry-fed flies, respectively; Figure 4—figure supplements 5 and 6). While these diet-distinctive metabolites did not always originate from fruit-specific metabolites and could be detected in other flies and other fruits (Figure 4—figure supplement 5), their quantities were lower there than in the focal fruit and flies who consumed it. It is worth noting that few diet-specific ions were produced de novo by flies (fruits intersection of degree zero: 0%, 5%, 5%, and 3% ions in blackcurrant, cherry, cranberry, and strawberry-fed flies, respectively), consistent with the metabolic generalism hypothesis.

Altogether, we found that quantitative levels of ions are critical to correctly classify fly metabolomes according to diet. Consistent with this finding, we observed that qualitative and quantitative datasets did not have the same resolving power when it came to distinguishing flies based on their diet (Figure 4—figure supplement 7). While randomly picking ~300 ions would lead to a 75% classification accuracy for flies’ diet when using their quantification levels, a similar performance was attained with a sampling of ~1000 ions when using only their presence. Regardless, flies’ diet could be readily inferred based on a relatively small subset of ions.

Identification and fate of metabolites associated with fruit diets

To gain a better understanding of the distinctive features of flies and their diet, we tried to identify diet-specific fly ions of the ‘compact’ list together with the 50 major ions (i.e. those having the largest peak area) for each investigated fruit. Manual curation and detailed mass spectra analysis allowed us to identify 71 metabolites, 26 of which were confirmed with commercial standards. Identified metabolites belonged to major plant metabolite families, including anthocyanins, flavonoids, organic and hydroxycinnamic acids, and terpenes (Supplementary file 1). A two-dimensional clustering analysis of metabolites associated with diet illustrates that even a limited set of these compounds was sufficient to infer flies’ diet (Figure 5). A survey of the published literature showed that many of the metabolites identified here in specific fruits (and flies that were grown on them) had already been detected and identified in the same fruits (Figure 5, Supplementary file 1), thereby supporting their correct identification.

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Depending on fruits and specific metabolites, relative amounts of fruit-derived metabolites detected in flies did not necessarily mirror their relative abundance in fruits (Figure 5—figure supplement 1). Indeed, some major fruit metabolites, such as the anthocyanins delphinidin in blackcurrant, cyanidin in cherry, or pelargonidin in strawberry, were detected in flies, albeit with a relatively low relative abundance (fly/fruit ratio between 0.01 and 0.001). Conversely, other less abundant fruit metabolites, such as terpenes, were relatively abundant in flies (fly/fruit ratio >0.5). Despite the relatively low number of identified metabolites, our quantification results demonstrate that only some fruit metabolites are metabolized (or excreted), while others tend to accumulate in flies.

As expected from previous studies, organic acids tended to be shared by all fruits, but with a particular balance depending on fruits: malic, quinic, and citric acids were always present in fruits (and flies) but with elevated levels in cherry, cranberry, and blackcurrant fruits (and flies that consumed them), respectively. Another chemical family ubiquitous in plants are flavonoids, with many potential physiological effects for consumer organisms, such as neurobehavioral modulation of activity (Bugel and Tanguay, 2018), feeding, and oviposition (Simmonds, 2001; Treutter, 2006). All fruits harbored major flavonoids such as quercetin, kaempferol, or myricetin, with specific substituent groups: quercetin arabinoside and rhamnoside in cranberry, quercetin rutinoside in cherry, quercetin glucoside in blackcurrant and quercetin glucuronide in strawberry. Those substituents have been shown to modulate the bioactivity of flavonoids (Bugel and Tanguay, 2018) and might mediate differential developmental responses to fruit diet in D. suzukii (Olazcuaga et al., 2019). While these substituents can undergo profound modifications by the gut microbiome (e.g. hydrolysis), we found no large-scale trace of microbiota influence in the present study, with flavonoids being essentially carried ‘as is’ in flies’ metabolomes. As an interesting subclass of flavonoids, major anthocyanins characteristic of the investigated fruits (and of their color) were readily found in flies that consumed these fruits. Strawberry-fed flies displayed elevated levels of pelargonidin glucoside, the main anthocyanin of strawberry fruits (da Silva et al., 2007). Similarly, cranberry- and cherry-fed flies presented high levels of cyanidin arabinoside, and cyanidin glucoside and rutinoside, the main anthocyanins found in cranberry and cherry, respectively (Acero et al., 2019; Seeram et al., 2004). Finally, fruits and flies that consumed them also displayed specific chemical signatures associated with terpenoids, considered as the largest class of plant secondary metabolites (Dudareva et al., 2004). Our results show that blackcurrant-fed flies can easily be discriminated by their levels in some linalool derivatives. While this volatile, floral-scented monoterpene is found in many plant families (Knudsen et al., 2006; Pichersky and Lewinsohn, 2011), specific linalool derivatives, e.g., carboxylinalool glycoside and linalooloxide glycoside, were predictive of the flies’ blackcurrant diet. Similarly, flies that developed on strawberry can be differentiated based on their elevated content in nerolidol, a sesquiterpene found in the floral scent of many plant families (Knudsen et al., 2006) and in fruits including strawberry (Aharoni et al., 2004).

While most of these signatures involve a passive accumulation of plant secondary metabolites, we also uncovered traces of the metabolization of fruit compounds. Indeed, we found elevated levels of hippuric acid in all flies, and particularly in cranberry-fed flies. Hippuric acid originates from the metabolization of various phenolic compounds (such as flavonoids and chlorogenic acids) by the gut microbiome and is a biomarker of fruit (and especially berries) consumption in various species including humans (De Simone et al., 2021; Ulaszewska et al., 2020). This result highlights that the metabolization process of major fruit compounds by D. suzukii may be relatively universal, and lack specificity, as shown by the accumulation of monoterpenes in blackberry-fed flies. However, it is noteworthy that some compounds belonging to other families of toxic plant metabolites do not seem to affect D. suzukii. Both cherry puree and cherry-fed flies were found to contain amygdalin, which belongs to the cyanogenic glucoside family. The toxicity of cyanogenic glucosides has been widely documented in the context of plant-insect interactions (Zagrobelny et al., 2004). However, cherry has been identified as an excellent host for D. suzukii, in both oviposition preference and larval performance experiments (Olazcuaga et al., 2019).

The direct comparison of metabolomes of fruits and of individuals that were grown on them sheds some light on basic issues pertaining to diet generalism (Forister et al., 2012). Indeed, we found that consumption by generalist individuals of dissimilar diets resulted in a diet-unspecific qualitative response to host biochemistry, i.e., ‘metabolic generalism.’ This tolerant reaction to diet also leads to the passive accumulation of diet-specific metabolites in individuals. As a result, while individuals were mostly similar across diets, detecting their particular diet was straightforward.

The biochemical composition of stone fruits, berries, and pseudocarps has been explored in numerous studies, highlighting the major contributions of sugars, organic acids, and secondary metabolites to the chemistry of fruits. Our untargeted overview of fruit composition enabled us to confirm that these fruits differ widely in their biochemical composition, and most importantly, that phylogenetic differences correspond to different biochemical landscapes for frugivorous species in our case. It is important to note, however, that the phylogenetic classification of the studied fruit species does not represent their proximity in terms of chemical composition. This strengthens the view that the taxonomic scale may not be the best scale to evaluate diet breadth and the adaptive challenges posed by generalism. For herbivores, it is also important to consider which plant organs are consumed (roots, leaves, fruits), as their respective composition may offer different dietary challenges and different proximities between plant species.

The use of diverse hosts had a variety of biochemical consequences on individuals of a generalist species, all consistent with the ‘metabolic generalism’ hypothesis. Indeed, diet-specific metabolites were rare, most fruit metabolites were incorporated in all individuals regardless of diet and overall metabolite pattern indicated a proximity across all insect samples. On the one hand, individuals showed a remarkably fixed qualitative chemical response to diet, coherent with a canalized response. This pattern mirrored the metabolic homeostasis found in some generalist insects reared on various protein:carbohydrates (P:C) ratios (Silva-Soares et al., 2017; Watanabe et al., 2019; Young et al., 2018). On the other hand, different diets had a significant impact on the quantity of a multitude of ions, resulting in the straightforward identification of insects’ diets based on their metabolome. Our study thus highlights that the physiological response to various diets, while generic in structure, was plastic when relative metabolite amounts were considered. This biochemical response could be expected from studies underlining the transcriptional plasticity in generalist species from all major insect clades (Birnbaum and Abbot, 2020; Celorio-Mancera et al., 2016; Celorio-Mancera et al., 2012; Celorio-Mancera et al., 2013; Christodoulides et al., 2017; Ragland et al., 2015; Simon et al., 2015).

The simultaneous observation of a single general qualitative response and diverse quantitative responses to diets is coherent with the metabolic generalism hypothesis and may help reconcile paradoxical notions about the consequences of generalism at the organismal level. On the one hand, individuals from generalist species do not always differ in response to various diets (e.g. Leptinotarsa decemlineata, Forister et al., 2007; or Lymantria dispar, Barbosa, 1978; Lazarevic et al., 1998). It is a defining characteristic of generalist species that they can tolerate (i.e. display relatively constant developmental responses under) a wider range of dietary circumstances when compared to specialist species. It makes sense, therefore, that the structural backbone of the metabolome of generalist individuals remains largely unaffected by diet, as uncovered here. On the other hand, the diverse quantitative responses of individuals’ metabolomes to diet highlight the passive metabolic response of generalist individuals to the idiosyncrasies of their dietary environment. In particular, we observed that distinctive fruit secondary metabolites, relating to their specific flavor (flavonoids), color (anthocyanins), or scent (terpenoids), were accumulated in corresponding individuals, and that very few de novo diet-specific individuals’ metabolites were produced. This may be a common feature in generalist frugivores as they have to face the exceptional diversity of secondary metabolites found in fruits (Kessler and Kalske, 2018; Wetzel et al., 2020; Whitehead et al., 2022).

Our study thus suggests that diet generalization could stem from reduced attention to hosts’ biochemical peculiarities and a neutral, passive stance towards potential hosts. While most of the ecological and evolutionary studies of host-plant interactions have focused on intricate plant-insect relations relying on strong selective forces, a passive and generic metabolic response could help species extend their diet breadth, at least transiently on evolutionary timescales. In this case, diet generalism would originate from a general tolerance rather than from the accumulation of independent genetic features associated with the exploitation of different resources (Forister et al., 2012; but see Calla et al., 2017; Rane et al., 2019), and the resulting plastic quantitative response to the diet may not necessarily be adaptive.

Immediate costs of weakened defenses against specific plant compounds can be observed in generalist species (Ali and Agrawal, 2012). Here, the passive accumulation of terpenoids in blackcurrant-fed flies indicates that D. suzukii may not have evolved efficient monoterpene metabolization pathways. In addition to their attractant or deterrent properties (Binder and Robbins, 1997), some terpenes have been shown to exhibit toxic properties and to be subjected to detoxification pathways in insects (Blomquist et al., 2021; Scalerandi et al., 2018). Indeed, in D. suzukii, a blackcurrant diet causes a relatively high larval mortality and leads to the extinction of the population in only a couple of generations (Olazcuaga et al., 2019; Olazcuaga et al., 2021). However, other fruits harboring potentially harmful compounds, such as amygdalin in cherry, can be excellent hosts for D. suzukii, including elevated oviposition preference and larval performance (Olazcuaga et al., 2019). Therefore, metabolic generalism may not exclude some adaptations to cope with specific classes of toxic compounds, potentially reflecting the ancestral niche of generalist herbivores.

Metabolic generalism could also procure both immediate and longer-term benefits. For instance, the accumulation of flavonoids increases the fitness of some phytophagous species (e.g. Polyommatus icarus; Simmonds, 2003). While chemical sequestration is an active process in specialist species, passive mechanisms may be common in generalist species (Petschenka and Agrawal, 2016). Here, the probably passive ‘sequestration’ of flavonoids by generalist individuals might be useful against predators or parasitoids. On larger ecological scales, metabolic generalism could also entail benefits, e.g., by enabling a geographical expansion triggering enemy-release or by reducing intra-guild competition. When successive generations of herbivores must exploit different hosts seasonally (e.g. in frugivores), an immediate reward of metabolic generalism could stem from resource allocation alternatives, e.g., a homeostatic immune response.

The passive accumulation of plant metabolites, such as anthocyanins, may also illustrate a greater opportunity for diet generalism due to plant domestication, especially for frugivorous species (Whitehead et al., 2017). Indeed, anthocyanins are known to trade-off with plant defense systems, and the domestication of fruit crops, by acting on anthocyanins accumulation, may have lowered plant defenses and thereby allowed generalist species to exploit niches that were ancestrally too challenging. For instance, it has been demonstrated that the domestication of cranberry cultivars, by selecting upon anthocyanin-related traits such as ripening and fruit color intensity, resulted in lowered plant defenses responses related to the jasmonic acid pathway (Rodriguez-Saona et al., 2011). In strawberries, it is known that biochemical insect resistance traits correlate negatively with important agronomical traits such as yield (Hancock et al., 2008). On the contrary, blackcurrant domestication mainly focused on plant pathogens and frost resistance for much of its history (Brennan, 2008), and this could explain the high levels of detrimental terpenoids in this species. Overall, biochemical changes induced by plant domestication are expected to lead to (i) increased diet generalism and (ii) increased levels of non-lethal plant secondary metabolites in herbivores, especially in frugivores.

Finally, by showing that fruit-specific metabolites were readily found in metabolomes, our study suggests that metabolomic data might help track the diet of phytophagous insects in the wild (Alberdi et al., 2019; Nielsen et al., 2018). This could complement high-throughput DNA sequencing-based diet reconstruction, which relies on the presence of foreign DNA material. Prerequisites for achieving this goal include an increased ability to correctly identify plant secondary metabolites and laboratory experiments to study the effect of various diets on the herbivores’ metabolomes during development.

In the future, the investigation of different spatial and temporal scales in resource use could help to shed light on the equilibrium between diet generalism and specialization (Devictor et al., 2010), and on the origins and limits of diet generalism (Bolnick et al., 2003; Roughgarden, 1972; Sexton et al., 2017). To date, the interaction of phytophagous insect species such as leaf-chewing and mining insects with their host plants has drawn much of the research attention. Compared to more general plant tissues, fruits are specialized organs interacting with multiple species, with detrimental or beneficial impacts to plant fitness, and this may have shaped a greater complexity of the chemical landscape in fruits (Cipollini and Levey, 1997). If the response to insect pests tends to decrease the attractiveness or palatability of fruits for more desirable seed dispersers, such as vertebrate frugivores, anti-insect defenses may perturb the reproductive potential of host plants (Andersen, 1988; but see Wilson et al., 2012). Understanding the ecological constraints exerted on both the chemistry of fruits and the physiology of their consumers, impacting the evolution of niche breadth itself, will require a detailed knowledge of molecular- to community-level interactions across multiple trophic levels.

All data & code generated during this study have been deposited in the INRAE dataverse. The shiny application enabling the exploration and analysis of our complete dataset (PCA, GLM/Elastic Net and associated visualizations) is available here.

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Decision letter after peer review:

Thank you for submitting your article "Metabolic consequences of various fruit-based diets in a generalist insect species" for consideration by eLife. Your article has been reviewed by 3 peer reviewers, one of whom is a member of our Board of Reviewing Editors, and the evaluation has been overseen by Meredith Schuman as the Senior Editor. The reviewers have opted to remain anonymous.

The reviewers have discussed their reviews with one another, and the Reviewing Editor has drafted this to help you prepare a revised submission.

On the basis of metabolomics methods, this manuscript identified the background of the generalization of insect dietary preferences based on a novel hypothesis which the authors termed the "general metabolism hypothesis". Many studies in this area focus on how plants and specialized insect herbivores counter-adapt, and the authors present an interesting approach. The following concerns must be resolved through revision before being published in eLife. Please respond only to these essential revisions in your response letter and your revision, which are determined from the consultative review process. In doing so you may refer to relevant comments from the individual reviews.

1) In this experiment, fruit extract was added to an artificial diet rather than (additionally) using various fruits, which decreases its ecological relevance. Moreover, it is questioned whether artificial diet contamination affects the insect metabolome data. This problem can be addressed by analyzing direct fruit feeding in addition to the artificial diet data.

2) It is also essential to address the concerns on the analysis process for metabolomics data raised by reviewer #3.

3) Moreover, as mentioned by reviewer #1, the excessive focus on the model organism limits understanding the value of the manuscript. This study requires further discussion regarding scalability from the perspective of a generalist's diet breath.

Reviewer #1 (Recommendations for the authors):

To emphasize the implication and novelty of this study, the authors should revise the flow of the manuscript according to the main research hypotheses. Detailed suggestions are as follows:

1) Introduction

– Research questions (L86~L90) should be rewritten according to the two main research hypotheses.

– The last paragraph in the Introduction section contains the summarized results of the study (L93~L96). This part should be removed or moved to the Discussion section.

2) Results

– Description of the contamination and sequestration (accumulation) of fruit-specific metabolites in the fly is not clearly separated. More description about these two aspects is needed.

– The premise of the PCA of the integral dataset (L185~L187) seems inappropriate because of the fundamental difference between plant (fruit) and animal (fly). Moreover, the fly diet contained not only fruit puree. Even if the diets are the main influence on flies' metabolomes, the default constituents of the fly body might make bias in the multi-component analysis. From that point, in Figures 1F and 1G, the expected results from the hypotheses are also inappropriate when the whole dataset and ions are used. Authors should modify the design of the analysis in Figures 1F and 1G, and interpret the results carefully.

3) Discussion

– As mentioned in the Introduction part, the phylogenetic relationship of the studied berries [blackcurrant (Grossulariaceae), cherry and strawberry (Rosaceae), and cranberry (Ericaceae)] should be discussed to assess the phylogenetic diet breadth. Metabolomic profiles as in PCA results do not correspond to the phylogenetic relationship of the four studied species.

– Probable mechanism of the diet generalism of studied species is described well. On the other hand, the overall readability could be enhanced by rearrangement of the paragraphs according to the description of the results or design of Figure 1.

– The last two paragraphs seemed to be far from the main research context. If the authors intended to discuss the plant domestication and metabolism of fly, developed phenotypes during domestication about all studied species should be more discussed.

4) Conclusion

– Overall sentences of the Conclusion section do not correspond to the main context. Except for the first sentence, sentences seem to be appropriate to be Introduction section. Authors should re-write the conclusion from the key finding and implications of the research.

Reviewer #3 (Recommendations for the authors):

1. Comparing the diet metabolome and frass metabolome of D. suzukii would provide cleaner results without interference from the insect metabolites. On the same line, a proper control metabolome of D. suzukii fed on an artificial diet without fruits shall be included.

2. The authors simply merged positive mode data and negative mode data, however, many metabolites could be detected in both ionization modes, this redundancy would influence the number of shared ions, and thus, shall be further cleaned up before analysis.

3. In P8, line 121, the authors claimed "qualitative data alone enabled perfect discrimination between fruit", while in Figure 1—figure supplement 2, it seems that the great majority of ions (4996) are indiscriminate and shared among 4 fruits.

4. In P13, line 252, the authors stated that "A survey of the published literature showed that many of the metabolites identified here in specific fruits (and flies that were grown on them) had already been detected and identified in the same fruits (Figure 5 & Supplementary Table 1), thereby supporting their correct identification." I don't see these are evidence of correct identification, at least an MS/MS comparison shall be provided to support these annotations.

[Editors' note: further revisions were suggested prior to acceptance, as described below.]

Thank you for resubmitting your work entitled "Metabolic consequences of various fruit-based diets in a generalist insect species" for further consideration by eLife. Your revised article has been evaluated by Meredith Schuman (Senior Editor) and a Reviewing Editor.

This important study uses untargeted metabolomics to help us understand how some herbivores are able to be generalists, rather than specializing in the metabolism of specific plant species. This is an important area, since little is known about how generalist insect species metabolize their food. Particularly, this study provides a valuable global chemical comparison of how diverse diet metabolites are processed by a generalist insect species. The evidence, potentially solid, is currently incomplete: see the remaining comments below.

The majority of concerns raised by reviewers were addressed effectively. In spite of this, the method section is too simplified and does not provide enough information to readers, as well as the fact that artificial diet control analysis and results were not provided – the supplementary information should at least include this information.

On the basis of metabolomics methods, this manuscript identified the background of the generalization of insect dietary preferences based on a novel hypothesis which the authors termed the "general metabolism hypothesis". Many studies in this area focus on how plants and specialized insect herbivores counter-adapt, and the authors present an interesting approach. The following concerns must be resolved through revision before being published in eLife. Please respond only to these essential revisions in your response letter and your revision, which are determined from the consultative review process. In doing so you may refer to relevant comments from the individual reviews.

We thank the Editor and Reviewers for their consideration of our manuscript. We agree that the main originality of our work is the joint analysis of plants’ and herbivores’ chemistries and we tried to improve our manuscript according to the referees’ suggestions. Please find our detailed responses to all comments below (lines numbers correspond to the manuscript with highlighted changes file).

1) In this experiment, fruit extract was added to an artificial diet rather than (additionally) using various fruits, which decreases its ecological relevance.

We agree with the Editor and Reviewers that using natural fruits in our experiment would have increased the ecological relevance of our study. However, previous experiments by our group showed that artificial fruit media provide a relatively accurate sensorial representation of the actual fruits individuals encounter in the field. Indeed, Olazcuaga et al. 2022 found that female oviposition preference and larval performance was higher on artificial fruit medium corresponding to the fruit from which the individuals originated than on fruit media corresponding to other fruits.

In addition, we chose to use fruit purees supplemented with a baseline artificial diet for the following reasons:

1. In many dipteran species and Drosophila species in particular, fruits alone do not provide all the chemical compounds necessary for larval development. Specifically, proteins are mainly harvested from microorganisms. While natural fruits would have provided such elements to our larval and adult flies, it would have been impossible to control for a homogenous input of proteins between fruits and among replicates. Besides protein input, natural microorganisms would probably alter other aspects of fruit composition, together with consumers’ microbiota. Such uncontrolled cascading effects would be difficult to account for, and reaching a conclusion about our main question could have been impossible.

2. We used fruit purees that were as close as possible to natural fruits: while they were industrially produced in order to allow for a homogeneous composition between replicates, all fruit purees were organic, and the transformation steps only included mechanical transformation and pasteurization. In particular, no sugars, coloring, or preservatives were added to fruit purees.

3. While an artificial diet basis was included in our rearing media, its share was kept to a minimum, since our recipe is 60% of fruit puree and 40% of the artificial diet. Our artificial media are thus far from the standard media used in regular laboratory rearing procedures.

4. The composition of the artificial part of our fruit media was relatively simple, consisting mainly of yeast-based protein sources.

We thus agree that the ecological relevance of our study would have improved by using of natural fruit. However, to reach firm conclusions about the metabolic processes underpinning generalist diets in insects, we needed to maintain controlled dietary inputs throughout the insects’ development. We consider that our choice of an artificial medium consisting largely of natural fruits is the preferable balance between controlled experimental procedures and ecological relevance. We now include modifications l479-487 to better explain this point.

We also wish to note that while experimental evaluation of the interaction between bacterial communities, fruits, and their consumers was beyond the scope of our present study, the addition of this ecologically relevant layer of complexity constitutes a captivating avenue for future research. We could add this perspective to our manuscript if the Editor/Reviewers consider it noteworthy.

Moreover, it is questioned whether artificial diet contamination affects the insect metabolome data. This problem can be addressed by analyzing direct fruit feeding in addition to the artificial diet data.

Because some chemical inputs are required from the artificial media (e.g., proteins) to complete insects’ development, it is true that this artificial diet component is included in the insects’ metabolome.

However, using an artificial diet component with industrial yeast enabled us to certify that all fruits and replicates are homogeneous regarding these elements. Therefore, the only variation in the diets of all insects was the fruit component, with all other elements being equal and consistent. This allowed a direct comparison between diets and their effect on insects’ metabolomes.

As stated before, we think that direct fruit feeding could either:

• mix relative contributions of microorganisms and fruit content to the insects’ metabolomes, with unknown variance between replicates, if fruits are not controlled for their bacterial content,

• fail to complete the insects’ development if fruits are rid of their bacterial content.

We thus feel that direct fruit feeding may not be the appropriate procedure to exclude the effect of the artificial component of the diet from the insects’ metabolomes. Additional layers of biological complexity could add much noise to the experimental data and preclude any conclusion if not considered/controlled for.

Another way to control whether the artificial diet could alter our conclusion regarding the effect of fruit on the insect metabolome is by including insects that have only experienced the artificial diet. As stated in more details below, we did include such controls in our original experiment, at each generation. The inclusion of such control individuals did not alter our conclusions (see below). We modified our manuscript to include this result (l.110-113 in the Results section and l.584-589 in the Methods section), which will certainly strengthen the reader’s confidence about the relevance of the study.

2) It is also essential to address the concerns on the analysis process for metabolomics data raised by reviewer #3.

The first concern of Reviewer #3 on the analysis process regards our ability to interpret patterns when “fruit-derived” metabolites and “insect-derived” metabolites are mixed together. We now explain that proper fly controls were processed and illustrate below that their inclusion in the dataset results in similar patterns and identical conclusions. Please find a detailed answer in the Reviewer #3 section.

The second concern of Reviewer #3 regards our methodology for peak selection. We now detail our procedure and explain our choice of threshold in the Reviewer #3 section.

The third concern regards our methodology for peak annotation. We are now providing MS2 data as recommended by Reviewer #3 and present our annotation results in full detail in Supplementary Table 1. Please find a detailed answer in the Reviewer #3 section.

3) Moreover, as mentioned by reviewer #1, the excessive focus on the model organism limits understanding the value of the manuscript. This study requires further discussion regarding scalability from the perspective of a generalist's diet breath.

We agree with the Editor/Reviewers on this important comment. We thus modified our Discussion accordingly and took care to use terms for which each point could be made at the correct scale (most of which are herbivores or frugivores, see Discussion). The peculiarity of our model system is now only discussed in a single occasion and serves as an example (l.387-396). We feel that our Discussion section and its biological value has been significantly enhanced by this comment.

Reviewer #1 (Recommendations for the authors):

To emphasize the implication and novelty of this study, the authors should revise the flow of the manuscript according to the main research hypotheses. Detailed suggestions are as follows:

1) Introduction

– Research questions (L86~L90) should be rewritten according to the two main research hypotheses.

We have rewritten the (now) last paragraph of the introduction section accordingly (l.86-93).

– The last paragraph in the Introduction section contains the summarized results of the study (L93~L96). This part should be removed or moved to the Discussion section.

The previously last paragraph of the Introduction section has now been removed, according to the comment. We modified it to be able to move it in discussion.

2) Results

– Description of the contamination and sequestration (accumulation) of fruit-specific metabolites in the fly is not clearly separated. More description about these two aspects is needed.

We have extended the corresponding paragraph according to the Reviewers’ comment (l.136-146).

– The premise of the PCA of the integral dataset (L185~L187) seems inappropriate because of the fundamental difference between plant (fruit) and animal (fly). Moreover, the fly diet contained not only fruit puree. Even if the diets are the main influence on flies' metabolomes, the default constituents of the fly body might make bias in the multi-component analysis. From that point, in Figures 1F and 1G, the expected results from the hypotheses are also inappropriate when the whole dataset and ions are used. Authors should modify the design of the analysis in Figures 1F and 1G, and interpret the results carefully.

It may be the only point where we slightly disagree with Reviewer #1 on a minor aspect of this question, but still agree with her/his overall comment and performed the desired modifications.

From the point of view of the investigative technique of LC-MS, there is no fundamental difference between plant and animal metabolites. The methodology used here is totally blind to the nature of the processed samples (plant, animal or others), and simply recapitulates their chemical composition, in a standard way.

We agree with Reviewer #1 that fruits are not the only component in the fruit media and have addressed this point in detail below (see answers to Reviewer #3). Briefly, we now show the Editor & Reviewers that accounting for the artificial medium component of flies’ diet does not modify our results.

In particular, regarding Figure 1F & 1G, we show below that controlling for the artificial medium component of the flies’ diet has little impact on our results: while differently fed flies are slightly more dispersed, they still constitute a single cluster, and conclusions drawn from this analysis remain. With this controlled data, we show that the observed clustering of flies is not derived from the addition of a small proportion of artificial medium to their diet, but is derived from metabolites that originate directly or indirectly from fruits.

We agree however that even if fruits are the main influence on flies’ metabolome, a PCA could display a much less caricatural view than illustrated in Figure 1G. We have thus modified Figure 1G to better represent what could be the case of ‘multi-host metabolic specialism’: in this case, basic fly metabolomes would still be apart from fruit metabolomes (i.e., separated on dimension 1) but the diversity of metabolomic responses to various diets would align them on their fruit on the second dimension (e.g., because of high levels of diet specific metabolites being produced). In the case of a single metabolomic response to all diets (i.e., ‘metabolic generalism’), flies would also cluster on the second dimension of the PCA (e.g., because of the production of common metabolites irrespective of diet). We modified the Figure 1 caption accordingly (l.1028-1032). We thank Reviewer #1 for this comment, which has improved the presentation of our hypotheses.

3) Discussion

– As mentioned in the Introduction part, the phylogenetic relationship of the studied berries [blackcurrant (Grossulariaceae), cherry and strawberry (Rosaceae), and cranberry (Ericaceae)] should be discussed to assess the phylogenetic diet breadth. Metabolomic profiles as in PCA results do not correspond to the phylogenetic relationship of the four studied species.

We would like to thank Reviewer #1 for this very interesting comment that we did not previously develop. Indeed, the biochemical signal between fruits does not match the phylogenetic signal of fruit species. We agree with Reviewer #1 that this observation has ample consequences when trying to study generalism, as taxonomy may not represent a good scale to measure adaptive challenges. We now have made this clearer in the revised version of the manuscript (i) by adding a new figure to better illustrate this observation (Figure 1—figure supplement 3), and (ii) by discussing this point as recommended (l.131-135 and 338-343).

– Probable mechanism of the diet generalism of studied species is described well. On the other hand, the overall readability could be enhanced by rearrangement of the paragraphs according to the description of the results or design of Figure 1.

We thank Reviewer #1 for their comment on our description of diet generalism. However, the discussion is now modified to address the editor's main comment: to be less focused on our specific D. suzukii results. Briefly, our Discussion section now articulates the following subjects that are of interest to a broad readership: diversity and taxonomy of fruit composition, generality of qualitative response and plasticity in quantitative response to various diets, impact on the understanding of paradoxical results in diet generalism literature, possible origin of diet generalism, possible costs and benefits of metabolic generalism, relation between insect generalism and plant domestication, technical possibility of diet tracing in the wild and a few perspectives for future research. We feel that this discussion already sweeps a wide spectrum of general issues in diet generalism and do not wish to overburden it.

We however tried to broaden the scope of all Discussion paragraphs by limiting the reference to the specific metabolism of our model species (only l.386-396 remaining), as well as including more references from plant and fruit biochemistry studies. In particular, we now cite the works of Whitehead et al. to better link our results with scientific communities working on the evolution of plant biochemistry and frugivores’ diet breadth.

– The last two paragraphs seemed to be far from the main research context. If the authors intended to discuss the plant domestication and metabolism of fly, developed phenotypes during domestication about all studied species should be more discussed.

We agree with Reviewer #1 that the previous last two paragraphs are less related to the main research question of diet generalism. We chose to maintain those paragraphs in the current version for the following reasons: (i) the paragraph of diet tracing is a small yet important contribution to the possible study of diet generalism in the wild using untargeted metabolomics, and (ii) we developed our point about plant domestication and generalism in the current version.

Briefly, our main point about plant domestication and a possible impact on herbivore generalism is that the biochemical features most seeked by human domesticators may trade-off with plant defenses. This was demonstrated by a meta-analysis by Whitehead et al. (2017) that we now cite, and while this may not be true for all plant tissue, this was especially the case in fruits, and generally for harvested organs in crops. In turn, these biochemical changes are expected to lead to (i) increased generalism in frugivores and (ii) increased presence of non-lethal plant secondary metabolites in frugivores. We modified the corresponding Discussion paragraph accordingly (l.417-422).

4) Conclusion

– Overall sentences of the Conclusion section do not correspond to the main context. Except for the first sentence, sentences seem to be appropriate to be Introduction section. Authors should re-write the conclusion from the key finding and implications of the research.

write the conclusion from the key finding and implications of the research.

>> We agree that our previous Conclusions were rather perspectives and shortened and moved these sentences at the end of our Discussion section. We now provide a Conclusion that highlights how our study contributes to a deeper understanding of dietary generalism (l.454-459).

Reviewer #3 (Recommendations for the authors):

1. Comparing the diet metabolome and frass metabolome of D. suzukii would provide cleaner results without interference from the insect metabolites. On the same line, a proper control metabolome of D. suzukii fed on an artificial diet without fruits shall be included.

We agree with Reviewer #3 that frass metabolome would be an interesting addition to the data to better infer the excretion part of the metabolism of an herbivorous insect to a variety of diets. By observing distinctive fruit components that are accumulated, we here start to comprehend the metabolization process of various diets. We however feel that to avoid confounding effects, frass metabolome data would be better complemented with microbiota data, or even better, microbiota experimental control. This was beyond our primary objective to bring a large-spectrum biochemistry point of view to the community and would lead to a significantly larger amount of work. We feel that the venue underlined by Reviewer #3 is very promising for the future.

Regarding flies fed on an artificial diet without fruit, we did such proper controls (see above) and the inclusion of such controls did not modify our conclusions. We hope that the presentation of these results and the modification in the Results and Material and Methods sections (l.110-113; l.512-515, and l.583-589) will convince the Reviewer and all readers that our results do not depend on the presence of a fraction of artificial medium in the flies’ diet.

2. The authors simply merged positive mode data and negative mode data, however, many metabolites could be detected in both ionization modes, this redundancy would influence the number of shared ions, and thus, shall be further cleaned up before analysis.

We agree with Reviewer #3 that some metabolites could be detected in both ionization modes.

We thus tested whether restricting our analyses to a given ionization mode, positive or negative, would alter our results and conclusions. In Author response images 1-3 we show the Figures 2, 3 and 4 redrawn using either positive or negative modes. None of our results is significantly altered (same patterns of common and uncommon ions, same ability to discriminate flies based on their diet), so merging positive and negative datasets does not incur an important bias to our analyses and was kept. We now indicate that our analyses are robust to ionization mode in our manuscript (l.577-579).

Author response image 1

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Author response image 2

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Author response image 3

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3. In P8, line 121, the authors claimed "qualitative data alone enabled perfect discrimination between fruit", while in Figure 1—figure supplement 2, it seems that the great majority of ions (4996) are indiscriminate and shared among 4 fruits.

We agree with Reviewer #3 that the great majority of ions are shared among the four fruits. However, it is also possible to distinguish fruits based on the qualitative data alone. As indicated in our sentence and our Figure, several hundred ions are diagnostic of each fruit (from at least 287 to 650 private ions depending on the fruit). We modified our sentence to reflect that fruits also share a large part of their ions (l.127).

4. In P13, line 252, the authors stated that "A survey of the published literature showed that many of the metabolites identified here in specific fruits (and flies that were grown on them) had already been detected and identified in the same fruits (Figure 5 & Supplementary Table 1), thereby supporting their correct identification." I don't see these are evidence of correct identification, at least an MS/MS comparison shall be provided to support these annotations.

As stated previously, Supplementary Table 1 now details all information used for metabolite annotation: validation standard for 30 of 71 identified compounds, and MS/MS data comparison with mass spectral databases as well as with published literature. We now also provide an identification confidence level for each compound, as proposed by Schymanski et al. 2014 (full reference included in the metadata of Supplementary Table 1).

[Editors' note: further revisions were suggested prior to acceptance, as described below.]

This important study uses untargeted metabolomics to help us understand how some herbivores are able to be generalists, rather than specializing in the metabolism of specific plant species. This is an important area, since little is known about how generalist insect species metabolize their food. Particularly, this study provides a valuable global chemical comparison of how diverse diet metabolites are processed by a generalist insect species. The evidence, potentially solid, is currently incomplete: see the remaining comments below.

The majority of concerns raised by reviewers were addressed effectively. In spite of this, the method section is too simplified and does not provide enough information to readers, as well as the fact that artificial diet control analysis and results were not provided – the supplementary information should at least include this information.

We thank the Associate Editor and the Reviewing Editor for their comments. We fully understand the absolute necessity of providing the readers all information for correct assessment and replication of our study. This is especially true for the artificial diet control analysis and results, that are crucial to our study. That is why we now provide the artificial diet control analysis in full and in the main text, together with the raw data analysis in full in an Appendix. We have accordingly redrawn all figures of the main text to correspond to the artificial diet control analysis (all previous figures from the raw data analysis are included in the Appendix). We thus hope that the full inclusion of both analyses will enable the reader to correctly assess our evidence regarding the validation of our hypotheses.

We also tackled the first point mentioned by providing more information in our methods section. We now provide additional information regarding our food media preparation (l. l.447-470), origin of stock flies (l.481-488, 494-496), artificial diet control procedure (l.509-513; 587-597), processing of metabolomic data (l.562-567; 572-573) and host use analysis (l.634-642). All changes are highlighted in the corresponding docx file, and our current methods section is now 3749 words long. If Reviewing editors still think there is major information missing for this section, please do not hesitate to be specific in your demand, as we might have missed an important expectation.

Since previous comments asked specifically about the treatment of metabolomic data under XCMS, along with providing along the necessary procedure and the XCMS-processed datasets, we also now provide the raw metabolomic dataset before any XCMS treatment, on the dedicated Metabolights repository. While our data files are deposited and our accession number was edited and included in our manuscript, please be aware that validation and public disclosure usually occur after at least a week. Please also note that all code and datasets (both raw and artificial diet controlled) were updated in the dataverse repository and in the Shiny visualization application mentioned in our manuscript.

Author details

1. Laure Olazcuaga

   1. UMR CBGP (INRAE-IRD-CIRAD, Montpellier SupAgro), Campus International de Baillarguet, Montferrier, France
   2. Department of Agricultural Biology, Colorado State University, Fort Collins, United States

   Contribution

   Conceptualization, Resources, Funding acquisition, Investigation, Methodology, Writing – original draft, Writing – review and editing

   Contributed equally with

   Raymonde Baltenweck

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0001-9100-1305

2. Raymonde Baltenweck

   Université de Strasbourg, INRAE, Colmar, France

   Contribution

   Conceptualization, Resources, Data curation, Validation, Investigation, Methodology, Writing – original draft, Writing – review and editing

   Contributed equally with

   Laure Olazcuaga

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-8228-1517

3. Nicolas Leménager

   UMR CBGP (INRAE-IRD-CIRAD, Montpellier SupAgro), Campus International de Baillarguet, Montferrier, France

   Contribution

   Conceptualization, Resources, Investigation, Methodology, Writing – original draft, Writing – review and editing

   Competing interests

   No competing interests declared

4. Alessandra Maia-Grondard

   Université de Strasbourg, INRAE, Colmar, France

   Contribution

   Conceptualization, Resources, Validation, Investigation, Methodology

   Competing interests

   No competing interests declared

5. Patricia Claudel

   Université de Strasbourg, INRAE, Colmar, France

   Contribution

   Conceptualization, Resources, Investigation, Methodology

   Competing interests

   No competing interests declared

6. Philippe Hugueney

   Université de Strasbourg, INRAE, Colmar, France

   Contribution

   Conceptualization, Resources, Supervision, Funding acquisition, Validation, Investigation, Methodology, Writing – original draft, Project administration, Writing – review and editing

   Contributed equally with

   Julien Foucaud

   Competing interests

   No competing interests declared

7. Julien Foucaud

   UMR CBGP (INRAE-IRD-CIRAD, Montpellier SupAgro), Campus International de Baillarguet, Montferrier, France

   Contribution

   Conceptualization, Resources, Software, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Writing – original draft, Project administration, Writing – review and editing

   Contributed equally with

   Philippe Hugueney

   For correspondence

   julien.foucaud@inrae.fr

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0003-2272-3149

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