The human intestinal microbiota is composed of 10 13 to 14 microorganisms whose collective genome (“microbiome”) contains at least 100 times as many genes our own genome. We analyzed ∼78 million base pairs unique DNA sequence and 2062 polymerase chain reaction–amplified 16 S ribosomal sequences obtained from the fecal DNAs two healthy adults. Using metabolic function analyses identified genes, we compared with average content previously sequenced microbial genomes. Our microbiome has...

The distal human intestine harbors trillions of microbes that allow us to extract calories from otherwise indigestible dietary polysaccharides. products polysaccharide fermentation include short-chain fatty acids are ligands for Gpr41, a G protein-coupled receptor expressed by subset enteroendocrine cells in the gut epithelium. To examine contribution Gpr41 energy balance, we compared Gpr41-/- and Gpr41+/+ mice were either conventionally-raised with complete microbiota or reared germ-free...

Animals have developed the means for supporting complex and dynamic consortia of microorganisms during their life cycle. A transcendent view vertebrate biology therefore requires an understanding contributions these indigenous microbial communities to host development adult physiology. These are most obvious in gut, where studies gnotobiotic mice disclosed that microbiota affects a wide range biological processes, including nutrient processing absorption, mucosal immune system, angiogenesis,...

Our colons harbor trillions of microbes including a prominent archaeon, Methanobrevibacter smithii. To examine the contributions Archaea to digestive health, we colonized germ-free mice with Bacteroides thetaiotaomicron, an adaptive bacterial forager polysaccharides that consume, or without M. smithii sulfate-reducing bacterium Desulfovibrio piger. Whole-genome transcriptional profiling B. combined mass spectrometry, revealed that, unlike D. piger, directs thetaiotaomicron focus on...

The human gut is home to trillions of microbes, thousands bacterial phylotypes, as well hydrogen-consuming methanogenic archaea. Studies in gnotobiotic mice indicate that Methanobrevibacter smithii, the dominant archaeon ecosystem, affects specificity and efficiency digestion dietary polysaccharides, thereby influencing host calorie harvest adiposity. Metagenomic studies microbial communities genetically obese their lean littermates have shown former contain an enhanced representation genes...

Significance Caenorhabditis elegans is a major model organism, both from the pathogenesis dimension and also for metabolism, aging, developmental biology perspectives. And yet, its natural ecology, most especially, microbiome, almost untouched. Here we establish microbial community of C. . Using extensive culture collections, categorize spectrum responses (from antagonistic to beneficial) wide breadth wild bacteria with nearly 80% isolates supporting robust growth. In wild, specific microbes...

The nematode Caenorhabditis elegans is used as a central model system across biological disciplines. Surprisingly, almost all research with this worm performed in the absence of its native microbiome, possibly affecting generality obtained results. In fact, C. microbiome had been unknown until recently. This review brings together results from first three studies on microbiomes, published 2016. Meta-analysis data demonstrates considerable conservation composition microbial communities,...

The initial acquisition and early development of the intestinal microbiome during infancy are important to human health across lifespan. Mode birth, antibiotic administration, environment care, nutrition have all been shown play a role in assembly life. For preterm infants, who disproportionately at risk inflammatory disease (i.e., necrotizing enterocolitis), unique set clinical factors influence establishment microbiome. purpose this study was establish nutritional exposures on cohort...

The study of microbiomes by sequencing has revealed a plethora correlations between microbial community composition and various life-history characteristics the corresponding host species. However, inferring causation from correlation is often hampered sheer compositional complexity microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships host-microbiome systems. Yet available suffer several drawbacks, such as artificial...

Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to establishment of distinct physiological environments. However, determinants stability and variation these types remain largely undefined. Here, we use free-living nematode Caenorhabditis elegans identify natural among wild strains C. that drives microbiomes. To achieve this, first established a diverse model represents strain-level phylogenetic diversity naturally encountered wild. Using this...

The gut microbiota is essential for maintenance and repair of the intestinal epithelial barrier. As shifts in both barrier function composition are found inflammatory bowel disease patients, it critical to understand role distinct bacteria regulating repair. We identified a mouse commensal E. coli isolate, GDAR2-2, that protects mice from Citrobacter rodentium infection dextran sulfate sodium-induced colitis. Colonization with GDAR2-2 resulted expansion CX3CR1+ mononuclear phagocytes,...

While numerous health-beneficial interactions between host and microbiota have been identified, there is still a lack of targeted approaches for modulating these interactions. Thus, we here identify precision prebiotics that specifically modulate the abundance microbiome member species interest. In first step, show defining by compounds are only taken up target but no other in community usually not possible due to overlapping metabolic niches. Subsequently, use modeling two-member...

Bacterial nanocellulose (BNC) is a promising dietary fiber with potential as functional food additive. We evaluated BNC fibers (BNCf) in the Caenorhabditis elegans model to obtain insight into BNCf's biointeraction its gastrointestinal tract while reducing variables of higher complex animals. BNCf were uptaken and excreted by worms without crossing intestinal barrier, confirming biosafety regarding survival rate, reproduction, aging for concentrations up 34 μg/ml BNCf. However, slight...

Chronic exposure to high-fat diets (HFD) worsens intestinal disease pathology, but acute effects of HFD in tissue damage remain unclear. Here, we used short-term feeding a model injury and found sustained with increased cecal dead neutrophil accumulation, along dietary lipid accumulation. Neutrophil depletion rescued enhanced pathology. Macrophages from HFD-treated mice showed reduced capacity engulf neutrophils. Macrophage clearance neutrophils activates critical barrier repair...

ABSTRACT In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The cuticular surface serves as barrier and first point contact their microbial environments. this study, we identify microbes from natural habitats that associate its cuticle, constituting simple “skin microbiome.” We rear our animals on modified CeMbio, mCeMbio, consortium ecologically relevant microbes. combine standard microbiological methods an adapted micro skin-swabbing...

Abstract Background Skin-penetrating nematodes of the genus Strongyloides infect over 600 million people, posing a major global health burden. Their life cycle includes both parasitic and free-living generation. During generation, infective third-stage larvae (iL3s) actively engage in host seeking. develop reproduce on feces. At different points during their cycle, species encounter wide variety host-associated environmental bacteria. However, microbiome associated with species, behavioral...

Hydrogen peroxide (H 2 O ) is the most common chemical threat that organisms face. Here, we show H alters bacterial food preference of Caenorhabditis elegans , enabling nematodes to find a safe environment with food. induces leave patches laboratory and microbiome bacteria when those communities have insufficient -degrading capacity. The nematode’s behavior directed by -sensing neurons promote escape from bacteria-sensing attraction bacteria. However, input for removed enzymes neurons’...

Abstract The free-living nematode Caenorhabditis elegans remains one of the most robust and flexible genetic systems for interrogating complexities animal biology. Targeted manipulations, such as RNA interference (RNAi), CRISPR/Cas9- or array-based transgenesis, all depend on initial delivery nucleic acids. Delivery dsRNA by feeding can be effective, but expression in Escherichia coli is not conducive to experiments intended remain sterile with defined microbial communities. Soaking-based...

The microbiome is increasingly receiving attention as an important modulator of host health and disease. However, while numerous mechanisms through which the influences its have been identified, there still a lack approaches that allow to specifically modulate abundance individual microbes or microbial functions interest. Moreover, current for manipulation such fecal transfers often entail non-specific transfer entire communities with potentially unwanted side effects. To overcome this...

Escherichia coli encodes two DNA ligases, ligase A, which is essential under normal laboratory growth conditions, and B, not. Here we report potential functions of B. We found that across the entire Enterobacteriaceae family, B highly conserved in both amino acid identity synteny with genes associated oxidative stress. Deletion ligB sensitized E. to specific damaging agents antibiotics resulted a weak mutator phenotype, decreased biofilm formation. Overexpression caused dramatic extension...

Abstract In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The cuticular surface serves as barrier and first point contact this microbial milieux. Here, we identify microbes from natural habitats that associate its cuticle, constituting simple ‘skin microbiome’. We rear our animals on modified CeMbio, mCeMbio, consortium ecologically relevant microbes. combine standard microbiological methods an adapted micro skin-swabbing tool to...