Mechanistic Microbiome Studies: A Special Issue

Collection

1. 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 et al.

   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.
2. 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 et al.

   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.
3. 1. Microbiology and Infectious Disease

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

   Aaron G Wexler et al.

   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.
4. 1. Ecology

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

   Inés Martínez et al.

   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.
5. 1. Microbiology and Infectious Disease

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

   Manon Morin et al.

   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.
6. 1. Microbiology and Infectious Disease

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

   Sara C Di Rienzi et al.

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

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

   Richard R Stein et al.

   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.
8. 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 et al.

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

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

   Roman M Stilling et al.

   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.
10. 1. Microbiology and Infectious Disease

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

    Aspen T Reese et al.

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

    A selective gut bacterial bile salt hydrolase alters host metabolism

    Lina Yao et al.

    The deletion of a single gene encoding a selective bile salt hydrolase from the abundant human gut bacterium Bacteroides thetaiotaomicron significantly alters host metabolism.
12. 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 et al.

    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.