Cross-species comparisons of host genetic associations with the microbiome

Goodrich, Julia K.; Davenport, Emily; Waters, Jillian L.; Clark, Andrew G.; Ley, Ruth E.

doi:10.1126/science.aad9379

Cited by 239 publications

(213 citation statements)

References 40 publications

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“…The third possibility is likely the most acceptable one. At first, host genes shape the physiological environments as the "substrates" for microbes and the variations of "substrates" influence the gut microbial composition; then the metabolisms of gut microbiome affect the "substrates" in turn as feedback; finally, the interactions shape the host phenotype together 31,32 . The cecum has been easily overlooked because of its location at the posterior segment of the intestine.…”

Section: Discussionmentioning

confidence: 99%

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency

Yan

Sun

Yuan

et al. 2017

Sci Rep

206

195

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Interactions between the host and gut microbiota can affect gut metabolism. In this study, the individual performances of 252 hens were recorded to evaluate feed efficiency. Hens with contrasting feed efficiencies (14 birds per group) were selected to investigate their duodenal, cecal and fecal microbial composition by sequencing the 16S rRNA gene V4 region. The results showed that the microbial community in the cecum was quite different from those in the duodenum and feces. The highest biodiversity and all differentially abundant taxa between the different efficiency groups were observed in the cecal microbial community with false discovery rate (FDR) <0.05. Of these differentially abundant cecal microbes, Lactobacillus accounted for a greater proportion than the others. The abundances of Lactobacillus and Akkermansia were significantly higher while that of Faecalibacterium was lower (FDR < 0.05) in the better feed efficiency (BFE) group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis revealed that the functions relating to glycometabolism and amino acid metabolism were enriched in the cecal microbiota of the BFE group. These results indicated the prominent role of cecal microbiota in the feed efficiency of chickens and suggested plausible uses of Lactobacillus to improve the feed efficiency of host.The gastrointestinal tract is the major site of food digestion and nutrient absorption. Cecum is the chief functional section in the distal intestine, and its importance in birds' metabolism has received increasing attention 1,2 . The cecum, which is full of microbial fermentations, plays important roles in preventing pathogen colonization, detoxifying harmful substances, recycling nitrogen and absorbing additional nutrients 3 . The digestibility and the ability to metabolize crude fiber or other nutrients are lower in birds with a cecectomy than in normal birds 4 . In addition, significant absorption of glucose was observed in the cecum 5 , and a higher ability to actively absorb sugars at low concentrations was found in the cecum compared with the jejunum 6 . Located at the beginning of the intestine, the duodenum is crucial for feed digestion and absorption; it has a lower pH than the hindgut and is the region that absorbs most glucose 7 and other nutrients within the small intestine 8,9 . Although the cecum and the duodenum themselves are important, interactions between the gut and commensal microbes may exert a significant influence on the function of the intestine. Previous studies showed that the digestion of uric acid, cellulose, starch and other resistant carbohydrates in the cecum was associated with the cecal microbial members 3,10,11 . In a recent study, numerous oligosaccharide-and polysaccharide-degrading enzyme-encoding genes and several pathways involved in the production of short-chain fatty acids (SCFAs) were observed in the cecal metagenome of the chicken 12 . The SCFAs were produced mainly by microbial fermentation in the hindgut and could be a...

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Section: Discussionmentioning

confidence: 99%

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency

Yan

Sun

Yuan

et al. 2017

Sci Rep

206

195

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“…However, it has turned out that environmental factors are at least as important for shaping the overall composition [33]. The Firmicutes and Bacteroidetes phyla dominate the adult human gut microbiota, which remain relatively stable over time [34].…”

Section: In Utero (Me Af Pl)mentioning

confidence: 99%

The gut microbiota: An emerging risk factor for cardiovascular and cerebrovascular disease

2018

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Commensal gut microbiota have recently been implicated in cardiovascular disease (CVD) and cerebrovascular disease. Atherosclerotic plaque formation depends on the colonization status of the host. In addition to host nutrition and the related microbiota-dependent metabolic changes, activation of innate immune pathways triggers the development of atherosclerosis and supports arterial thrombosis. Gnotobiotic mouse models have uncovered that activation of Toll-like receptor-2 by gut microbial ligands supports von Willebrand factor-integrin mediated platelet deposition to the site of vascular injury. Depending on nutritional factors, the microbiota-derived choline-metabolite trimethylamine Noxide (TMAO) increases atherosclerotic plaque size, triggers prothrombotic platelet function and promotes arterial thrombus growth. Hence, the composition of the commensal microbiota is an emerging risk factor for CVD. Here, we provide an overview on microbiota-dependent pathomechanisms that drive the development of CVD and arterial thrombosis.Keywords: Arterial thrombosis r Atherosclerosis r Cardiovascular disease r Microbiota r Toll-like receptors IntroductionAt birth, our body surfaces are colonized by microbial communities (microbiota), representing one of the most densely colonized microbial ecosystems [1]. This process is strongly influenced by genetic, nutritional, and environmental factors [2]. The commensal microbiota constitutes a permanent inflammatory stimulus [3], which is kept in check by the host's immune responses [4]. The microbiota can be viewed as an organ that impacts host physiology [5,6]. Changes in gut microbiota composition were associated with intestinal diseases (e.g. inflammatory bowel disease, colon cancer) and cardiometabolic disease states, such as diet-induced obesity, type 2 diabetes, atherosclerosis, and arterial thrombosis [7]. The results from recent experimental and clinical studies have led to the assumption that Correspondence: Christoph Reinhardt e-mail: Christoph.Reinhardt@unimedizin-mainz.de molecules synthesized by the intestinal microbiota are involved in the development of cardiovascular disease (CVD) [8] and may increase the risk of arterial thrombosis [9, 10] as well as the outcome of ischemic stroke [11]. Experimental evidence from germ-free mouse studies and metagenomics analyses have associated the gut microbiota with obesity [12][13][14][15], type 2 diabetes [3, 16, 17], stroke [11, 18], and CVD [8, 9, 19]. Therefore, targeting the composition and metabolic function of the intestinal microbiota may represent a therapeutic option that in the future may allow prevention and treatment of cardiometabolic diseases [20].Here, we provide a comprehensive overview on the emerging link between gut microbiota and CVD. We delineate the contribution of this complex microbial ecosystem to metabolic inflammation and its impact on host metabolism. The main focus of this review is to highlight how gut microbiota may contribute to the development of CVD, cerebrovascular disease and arterial thromb...

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“…Bacteria are now considered key players in multiple aspects of the biology of multicellular organisms (1)(2)(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.…”

mentioning

confidence: 99%

Caenorhabditis elegans responses to bacteria from its natural habitats

Samuel

Rowedder

Braendle

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

347

479

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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,

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Cross-species comparisons of host genetic associations with the microbiome

Cited by 239 publications

References 40 publications

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency

The gut microbiota: An emerging risk factor for cardiovascular and cerebrovascular disease

Caenorhabditis elegans responses to bacteria from its natural habitats

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