The human intestinal microbiota is composed of 10 13 to 10 14 microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed ~78 million base pairs of unique DNA sequence and 2062 polymerase chain reactionamplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-Derythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.Our body surfaces are home to microbial communities whose aggregate membership outnumbers our human somatic and germ cells by at least an order of magnitude. The vast majority of these microbes (10 to 100 trillion) inhabit our gastrointestinal tract, with the greatest number residing in the distal gut, where they synthesize essential amino acids and vitamins and process components of otherwise indigestible contributions to our diet such as plant polysaccharides (1). The most comprehensive 16S ribosomal DNA (rDNA) sequencebased enumeration of the distal gut and fecal microbiota published to date underscores its highly selected nature. Among the 70 divisions (deep evolutionary lineages) of Bacteria and 13 divisions of Archaea described to date, the distal gut and fecal microbiota of the three ‡

The distal human intestine harbors trillions of microbes that allow us to extract calories from otherwise indigestible dietary polysaccharides. The products of polysaccharide fermentation include shortchain fatty acids that are ligands for Gpr41, a G protein-coupled receptor expressed by a subset of enteroendocrine cells in the gut epithelium. To examine the contribution of Gpr41 to energy balance, we compared Gpr41؊/؊ and Gpr41؉/؉ mice that were either conventionally-raised with a complete gut microbiota or were reared germ-free and then cocolonized as young adults with two prominent members of the human distal gut microbial community: the saccharolytic bacterium, Bacteroides thetaiotaomicron and the methanogenic archaeon, Methanobrevibacter smithii. Both conventionallyraised and gnotobiotic Gpr41؊/؊ mice colonized with the model fermentative community are significantly leaner and weigh less than their WT (؉/؉) littermates, despite similar levels of chow consumption. These differences are not evident when germ-free WT and germ-free Gpr41 knockout animals are compared. Functional genomic, biochemical, and physiologic studies of germ-free and cocolonized Gpr41؊/؊ and ؉/؉ littermates disclosed that Gpr41-deficiency is associated with reduced expression of PYY, an enteroendocrine cell-derived hormone that normally inhibits gut motility, increased intestinal transit rate, and reduced harvest of energy (short-chain fatty acids) from the diet. These results reveal that Gpr41 is a regulator of host energy balance through effects that are dependent upon the gut microbiota.host-microbial interactions ͉ energy balance ͉ enteroendocrine cells ͉ nutrient sensing ͉ polysaccharide fermentation O ur ability to effectively digest food reflects the combined activities of enzymes encoded in our primate genome and in the genomes of the trillions of microbes that reside in our distal guts. This microbial community, or microbiota, affects both sides of the energy-balance equation, influencing both the harvest of calories and the activity of host genes involved in the metabolism and storage of absorbed energy (e.g., ref.

Danio rerio ͉ symbiosis ͉ host-microbial cross-talk ͉ mice ͉ DNA microarrays

Our colons harbor trillions of microbes including a prominent archaeon, Methanobrevibacter smithii. To examine the contributions of Archaea to digestive health, we colonized germ-free mice with Bacteroides thetaiotaomicron, an adaptive bacterial forager of the polysaccharides that we consume, with or without M. smithii or the sulfate-reducing bacterium Desulfovibrio piger. Wholegenome transcriptional profiling of B. thetaiotaomicron, combined with mass spectrometry, revealed that, unlike D. piger, M. smithii directs B. thetaiotaomicron to focus on fermentation of dietary fructans to acetate, whereas B. thetaiotaomicron-derived formate is used by M. smithii for methanogenesis. B. thetaiotaomicron-M. smithii cocolonization produces a significant increase in host adiposity compared with monoassociated, or B. thetaiotaomicron-D. piger biassociated, animals. These findings demonstrate a link between this archaeon, prioritized bacterial utilization of polysaccharides commonly encountered in our modern diets, and host energy balance. adiposity ͉ energy homeostasis ͉ gut microbial ecology ͉ polysaccharide metabolism ͉ Methanobrevibacter smithii T he role of Archaea in human health remains unclear (1). One site where their influence may be profound is the gut. Hydrogen-consuming methanogenic archaeons are present in the intestinal tracts of many invertebrate and vertebrate species (2-4). Our adult intestine contains 10 trillion to 100 trillion microbial cells and is dominated by members of just two divisions of Bacteria, the Bacteroidetes and the Firmicutes (5). Archaea, the only known producers of methane, are present at high levels in 50-85% of humans (6-8). Concordance rates for methane production are equivalent for both monozygotic and dizygotic twins, underscoring the importance of family environment (mothers) in acquisition of methanogens (9). The most comprehensive enumeration of the adult human colonic microbiota reported to date (5) found a single predominant archaeal species, Methanobrevibacter smithii. This Euryarchaeote can comprise up to 10% of all anaerobes in the colons of healthy adults, while Methanosphaera stadtmanae and Crenarchaeotes can be minor members (10, 11).One manifestation of the mutualism between humans and their distal gut microbiota is that the latter extracts energy that would be lost from otherwise indigestible dietary polysaccharides (fiber). Fermentation of dietary fiber is accomplished by syntrophic interactions between microbes linked in a metabolic food web and is a major energy-producing pathway for members of the Bacteroidetes and the Firmicutes. These primary bacterial fermentors generate short-chain fatty acids (SCFAs), principally acetate, propionate, and butyrate, as well as other organic acids (e.g., formate) and gases [e.g., hydrogen (H 2 ) and carbon dioxide (CO 2 )]. Accumulation of H 2 inhibits bacterial NADH dehydrogenases, thereby reducing the yield of ATP. Studies in man-made bioreactors have shown that removal of H 2 by means of archaeal methanogenesis improves ferment...

Most Caenorhabditis elegans studies have used laboratory Escherichia coli as diet and microbial environment. Here we characterize bacteria of C. elegans' natural habitats of rotting fruits and vegetation to provide greater context for its physiological responses. By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety of bacteria in C. elegans habitats, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria being most abundant. From laboratory assays using isolated natural bacteria, C. elegans is able to forage on most bacteria (robust growth on ∼80% of >550 isolates), although ∼20% also impaired growth and arrested and/or stressed animals. Bacterial community composition can predict wild C. elegans population states in both rotting apples and reconstructed microbiomes: alpha-Proteobacteria-rich communities promote proliferation, whereas Bacteroidetes or pathogens correlate with nonproliferating dauers. Combinatorial mixtures of detrimental and beneficial bacteria indicate that bacterial influence is not simply nutritional. Together, these studies provide a foundation for interrogating how bacteria naturally influence C. elegans physiology.Caenorhabditis elegans | host-microbe interactions | ecology B iological organisms constantly live in contact with other organisms in a complex web of ecological interactions, which include prey-predator, host-parasite, competitive, or positive symbiotic relationships. Bacteria are now considered key players in multiple aspects of the biology of multicellular organisms (1-3). The richness and importance of these interactions were so far neglected because laboratory biology had succeeded in simplifying and standardizing the environment of the model organisms, providing in most cases a single microbe as a food source, and not necessarily even a naturally encountered one. The many aspects of organismal biology that were shaped by evolution in natural environments are thus undetectable in the artificial laboratory environment and can only be revealed in the presence of other interacting species. Examples include feeding behavior, metabolism of diverse natural food sources, interactions with natural pathogens that have shaped the organism's immune system, behavioral traits, and regulation of development and reproduction. At the genomic level, many individual genes may not be required in a standard laboratory environment but their role may be revealed by using more diverse and relevant environments (4, 5).The nematode Caenorhabditis elegans is a typical example of a model organism that has been disconnected from its natural ecology: although the species has been studied intensively in the laboratory for half a century, its habitat and natural ecology-what it naturally feeds on, its natural predators and pathogens,

The human gut is home to trillions of microbes, thousands of bacterial phylotypes, as well as hydrogen-consuming methanogenic archaea. Studies in gnotobiotic mice indicate that Methanobrevibacter smithii, the dominant archaeon in the human gut ecosystem, affects the specificity and efficiency of bacterial digestion of dietary polysaccharides, thereby influencing host calorie harvest and adiposity. Metagenomic studies of the gut microbial communities of genetically obese mice and their lean littermates have shown that the former contain an enhanced representation of genes involved in polysaccharide degradation, possess more archaea, and exhibit a greater capacity to promote adiposity when transplanted into germ-free recipients. These findings have led to the hypothesis that M. smithii may be a therapeutic target for reducing energy harvest in obese humans. To explore this possibility, we have sequenced its 1,853,160-bp genome and compared it to other human gut-associated M. smithii strains and other Archaea. We have also examined M. smithii's transcriptome and metabolome in gnotobiotic mice that do or do not harbor Bacteroides thetaiotaomicron, a prominent saccharolytic bacterial member of our gut microbiota. Our results indicate that M. smithii is well equipped to persist in the distal intestine through (i) production of surface glycans resembling those found in the gut mucosa, (ii) regulated expression of adhesin-like proteins, (iii) consumption of a variety of fermentation products produced by saccharolytic bacteria, and (iv) effective competition for nitrogenous nutrient pools. These findings provide a framework for designing strategies to change the representation and/or properties of M. smithii in the human gut microbiota.archaeal-bacterial mutualism ͉ comparative microbial genomics ͉ functional genomics and metabolomics ͉ gnotobiotic mice ͉ human gut microbiota T he human gut microbiota is dominated by two divisions of bacteria, the Bacteroidetes and the Firmicutes, which together encompass Ͼ90% of all phylogenetic types (phylotypes). Archaea are also represented, most prominently by a methanogenic Euryarchaeote, Methanobrevibacter smithii, which comprises up to 10% of all anaerobes in the colons of healthy adults (1, 2).Complex dietary polysaccharides (fiber) and proteins are digested by enzymes encoded by genes in the microbial community's collective genome (microbiome), but not in our human genome (3, 4). Bacterial fermentation of polysaccharides yields short chain fatty acids (SCFAs) (principally acetate, propionate, and butyrate), other organic acids (e.g., formate), alcohols (e.g., methanol and ethanol), and gases [e.g., hydrogen (H 2 ) and carbon dioxide (CO 2 )]. Host absorption of SCFAs provides up to 10% of daily caloric intake, although this value varies depending on the glycan content of the diet (5). Archaeal methanogenesis improves the efficiency of polysaccharide fermentation in animal gut ''bioreactors'' by preventing the buildup of H 2 and other reaction end products (6).Several recent obs...

Mitochondrial function is challenged by toxic byproducts of metabolism as well as by pathogen attack1,2. Caenorhabditis elegans normally responds to mitochondrial dysfunction with activation of mitochondrial repair, drug detoxification, and pathogen-response pathways1–7. From a genome-wide RNAi screen, we identified 45 C. elegans genes that are required to upregulate detoxification, pathogen-response, and mitochondrial repair pathways after inhibition of mitochondrial function by drugs or genetic disruption. Animals defective in ceramide biosynthesis are deficient in mitochondrial surveillance, and addition of particular ceramides can rescue the surveillance defects. Ceramide can also rescue the mitochondrial surveillance defects of other gene inactivations, mapping these gene activities upstream of ceramide. Inhibition of the mevalonate pathway, either by RNAi or statin drugs also disrupts mitochondrial surveillance. Growth of C. elegans with a significant fraction of bacterial species from their natural habitat causes mitochondrial dysfunction. Other bacterial species inhibit C. elegans defense responses to a mitochondrial toxin, revealing bacterial countermeasures to animal defense.

Host-associated microbiomes influence host health. However, it is unclear whether genotypic variations in host organisms influence the microbiome in ways that have adaptive consequences for the host. Here, we show that wild accessions of Arabidopsis thaliana differ in their ability to associate with the root-associated bacterium Pseudomonas fluorescens, with consequences for plant fitness. In a screen of 196 naturally occurring Arabidopsis accessions we identified lines that actively suppress Pseudomonas growth under gnotobiotic conditions. We planted accessions that support disparate levels of fluorescent Pseudomonads in natural soils; 16S ribosomal RNA sequencing revealed that accession-specific differences in the microbial communities were largely limited to a subset of Pseudomonadaceae species. These accession-specific differences in Pseudomonas growth resulted in enhanced or impaired fitness that depended on the host’s ability to support Pseudomonas growth, the specific Pseudomonas strains present in the soil and the nature of the stress. We suggest that small host-mediated changes in a microbiome can have large effects on host health.