Mechanistic Microbiome Studies: A Special Issue

The microbiome encompasses all the microorganisms within a specific environmental niche, ranging from animal guts to plant root systems. Its investigation has important implications for the study of disease and behaviour.

To highlight recent advances in the mechanistic understanding of microbiome function, eLife is pleased to present a Special Issue on this topic. This issue presents a collection of highly influential research relating to metagenomics, microbiota, and computational tools, as selected for publication by a specially convened group of experts.

We continue to welcome high-quality research on this topic on an ongoing basis.

Visit our main subject page to explore articles in the wider field of Microbiology and Infectious Disease and sign up to receive the latest research.

Collection

1. 1. Biochemistry and Chemical Biology
   2. Structural Biology and Molecular Biophysics

   Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme

   Lindsey RF Backman, Yolanda Y Huang ... Catherine L Drennan

   The common post-translational modification trans-4-hydroxy-L-proline is reversed by gut microbes with the help of hydroxyproline dehydratase (HypD), an enzyme that performs a radical chemical mechanism.
2. 1. Microbiology and Infectious Disease

   Gut microbiota density influences host physiology and is shaped by host and microbial factors

   Eduardo J Contijoch, Graham J Britton ... Jeremiah J Faith

   The density of the gut microbiota influences the host immune system and adiposity, and can be therapeutically manipulated.
3. 1. Immunology and Inflammation
   2. Microbiology and Infectious Disease

   The Crohn’s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response

   Sydney Lavoie, Kara L Conway ... Ramnik J Xavier

   Gnotobiotic and conventional mouse models of the IBD ATG16L1T300A SNP reveal gene-microbiota-immune interactions.
4. 1. Computational and Systems Biology
   2. Microbiology and Infectious Disease

   Extensive transmission of microbes along the gastrointestinal tract

   Thomas SB Schmidt, Matthew R Hayward ... Peer Bork

   Microbial populations are continuous along the gastrointestinal tract, with increased transmission in colorectal cancer and rheumatoid arthritis patients.
5. 1. Microbiology and Infectious Disease

   Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature

   Fotini Kokou, Goor Sasson ... Itzhak Mizrahi

   Microbiome and transcriptomic profiling of genetically selected tropical fish with high and low tolerance to cold exposure revealed host control over microbiome composition and response to temperature changes.
6. 1. Immunology and Inflammation
   2. Microbiology and Infectious Disease

   A bacterial immunomodulatory protein with lipocalin-like domains facilitates host–bacteria mutualism in larval zebrafish

   Annah S Rolig, Emily Goers Sweeney ... Karen Guillemin

   Discovery of a secreted protein from resident gut bacteria that reduced intestinal innate immune responses which would otherwise simultaneously compromise both bacterial and host survival.
7. 1. Computational and Systems Biology
   2. Microbiology and Infectious Disease

   Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

   Kevin D'hoe, Stefan Vet ... Jeroen Raes

   Human gut bacteria alter their metabolism in response to each other's presence, which causes their community dynamics to deviate from predictions that are based on mono-culture data.
8. 1. Microbiology and Infectious Disease

   Human gut Bacteroides capture vitamin B₁₂ via cell surface-exposed lipoproteins

   Aaron G Wexler, Whitman B Schofield ... Andrew L Goodman

   The human gut bacterial lipoprotein BtuG binds vitamin B12 with femtomolar affinity, can remove vitamin B12 from human intrinsic factor, and is required for commensal fitness in the gut.
9. 1. Ecology

   Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly

   Inés Martínez, Maria X Maldonado-Gomez ... Jens Walter

   Experiments in ex-germ-free mice establish a measurable effect of colonization history on gut microbiota assembly, illuminating a potential cause for the high levels of unexplained individuality in host-associated microbial communities.
10. 1. Microbiology and Infectious Disease

    Changes in the genetic requirements for microbial interactions with increasing community complexity

    Manon Morin, Emily C Pierce, Rachel J Dutton

    Analysis of the global genetic requirements and gene expression changes in E. coli in the presence of a simple microbiome revealed pairwise and higher-order interactions, and underlying molecular mechanisms.
11. 1. Microbiology and Infectious Disease

    Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids

    Sara C Di Rienzi, Juliet Jacobson ... Ruth E Ley

    Comparisons between lactobacilli bacteria in the small intestine and those evolved in the lab reveal several modes of resistance to toxic fatty acids.
12. 1. Computational and Systems Biology
    2. Immunology and Inflammation

    Computer-guided design of optimal microbial consortia for immune system modulation

    Richard R Stein, Takeshi Tanoue ... Vanni Bucci

    A computational method is presented that quantifies the effect that specific bacteria in the gut have on the immune system and guides the design of therapeutically potent microbial consortia to cure auto-immune disease.
13. 1. Microbiology and Infectious Disease

    Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins

    Nitzan Koppel, Jordan E Bisanz ... Emily P Balskus

    A unique, widely distributed gut bacterial enzyme selectively metabolizes plant-derived cardiac glycoside drugs.
14. 1. Neuroscience
    2. Microbiology and Infectious Disease

    Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice

    Roman M Stilling, Gerard M Moloney ... John F Cryan

    Social-interaction impairment in germ-free mice is associated with a markedly altered transcriptional response to social novelty in the amygdala, as characterised by replacement of upregulation of common stimulus-induced pathways with upregulation of the splicing machinery.
15. 1. Microbiology and Infectious Disease

    Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut

    Aspen T Reese, Eugenia H Cho ... Lawrence A David

    Disturbing the microbiota with antibiotics alters gut redox state via changes in electron acceptor availability, setting the stage for post-antibiotic succession.
16. 1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    A selective gut bacterial bile salt hydrolase alters host metabolism

    Lina Yao, Sarah Craven Seaton ... A Sloan Devlin

    The deletion of a single gene encoding a selective bile salt hydrolase from the abundant human gut bacterium Bacteroides thetaiotaomicron significantly alters host metabolism.
17. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

    Xue-Song Zhang, Jackie Li ... Martin J Blaser

    Alteration of host gut microbiota by antibiotic exposure in early life remodeled host intestinal immune development and metabolism and enhanced the induction of type 1 diabetes in genetically predisposed animals.