Unravelling the effects of the environment and host genotype on the gut microbiome

Spor, Aymé; Koren, Omry; Ley, Ruth E.

doi:10.1038/nrmicro2540

Cited by 1,318 publications

(1,115 citation statements)

References 119 publications

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“…The GI tract of animals is one of the most complex microbial ecosystems on Earth, and it is continuously affected by factors associated with the host (Spor et al 2011, Van den Abbeele et al 2011 and the outside environment (Claesson et al 2012). This complexity has been an obstacle to study single independent factors associated with its changes over time and among different populations of animals (e.g., healthy and diseased).…”

Section: The Gi Microbiotamentioning

confidence: 99%

Gastrointestinal microorganisms in cats and dogs: a brief review

Garcia-Mazcorro¹,

Minamoto

2013

Arch. med. vet.

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RESUMENEl tracto gastrointestinal (GI) de animales contiene diferentes tipos de microorganismos conocido como la microbiota GI. Por mucho tiempo, la microbiota GI ha generado interés porque los microorganismos GI están involucrados en múltiples procesos fisiológicos en el hospedero, así perpetuando salud o enfermedad. Estudios recientes han demostrado que la microbiota GI de gatos y perros es tan compleja como en humanos y otros animales, revelado con el uso de tecnologías de secuencia modernas y otras técnicas moleculares. La microbiota GI incluye miembros de todos los tres dominios principales de vida (Archaea, Bacterias y Eucariotas), pero las bacterias son el grupo de microorganismos más abundante y metabólicamente activo. El estómago de gatos y perros esta principalmente poblado de Helicobacter spp., el cual en perros puede representar tanto como el 98% de toda la microbiota bacteriana en el estómago. El intestino delgado contiene una microbiota más diversa, conteniendo representantes de al menos cinco diferentes filos bacterianos (principalmente Firmicutes y Bacteroidetes). El intestino grueso contiene el grupo de bacterias más abundante (~10 11 células bacterianas por gramo de contenido intestinal), diverso (al menos diez diferentes filos han sido detectados) y metabólicamente relevante en el tracto GI. La mayoría de las bacterias en el intestino grueso son anaerobios estrictos, los cuales dependen de la fermentación de sustancias no digeridas para subsistir. Aunque estudios recientes han dilucidado las complejidades de la microbiota GI en gatos y perros, más investigación todavía es necesaria para encontrar maneras de manipular exitosamente los microorganismos GI para prevenir y/o tratar enfermedades GI.Palabras clave: gastrointestinal, microbiota, gatos, perros. SUMMARYThe gastrointestinal (GI) tract of animals contains different types of microorganisms known as the GI microbiota. The GI microbiota has long been of interest because of its involvement in multiple physiological processes in the host, influencing health or disease. Recent studies have shown that the GI microbiota of cats and dogs is as complex as the one present in humans and other animals, according to state-of-the-art sequencing technologies and other molecular techniques. The GI microbiota includes members of all three main life domains (Archaea, Bacteria, and Eukaryotes), with bacteria being the most abundant and metabolically active group of microorganisms. The stomach of cats and dogs is mainly inhabited by Helicobacter spp., which in dogs may account for as much as 98% of all gastric bacterial microbiota. The small intestine harbors a more diverse microbiota as it contains representatives from at least five bacterial phyla (mainly Firmicutes and Bacteroidetes). The large intestine harbors the most abundant (~10 11 bacterial cells per gram of intestinal content), diverse (at least 10 bacterial phyla have been identified) and physiologically relevant group of bacteria in the GI tract. Most bacteria in the large intestine are strict an...

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Section: The Gi Microbiotamentioning

confidence: 99%

Gastrointestinal microorganisms in cats and dogs: a brief review

Garcia-Mazcorro¹,

Minamoto

2013

Arch. med. vet.

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“…Distinct community structure and composition characterizes different vertebrate and invertebrate species in their natural environments, global microbiota and interspecies relatedness, reflecting host phylogeny and incorporating elements of developmental and nutritional specialization (Ley et al, 2008a, b;Ochman et al, 2010;Yidirim et al, 2010). Such complex interactions between deterministic (genetic and developmental), environmental and stochastic factors in the assembly and dynamics of vertebrate gut microbiota are being studied intensely, from fundamental ecological perspectives to its impact on host health and disease (Dethlefsen et al, 2006;Ley et al, 2006;Dethlefsen et al, 2007;Palmer et al, 2007;Ley et al, 2008a;Turnbaugh et al, 2009;Reid et al, 2011;Spor et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

“…Significant advances in understanding the individual roles of host and environmental factors on the composition of vertebrate gut microbiota have resulted from studies on genetically inbred mouse lines (reviewed in Spor et al (2011)). Such studies have used both conventionally reared and germ-free animals inoculated selectively with different bacterial isolates or natural microbiota samples.…”

Section: Introductionmentioning

confidence: 99%

Host genetic and environmental effects on mouse intestinal microbiota

et al. 2012

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The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strainspecific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.

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“…The total number of microbes residing in the human body, especially in the gut, outnumbers that of human cells [3]. A vast array of recent studies has identified many microbial enterotypes in the human gut [4], [5], [6], [7], [8], [9], [10] and their potential roles in immunity [5], [7], [8], development [8], digestion [9], and other functions [10].…”

Section: Introductionmentioning

confidence: 99%

An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

Kumar

Gupta

et al. 2016

Genomics, Proteomics &Amp; Bioinformatics

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Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (>23 kb) metagenomic DNA (260/280 ratio >1.8) with a good yield (55.8 ± 3.8 ng/mg of feces). We also confirm that there is very low human genomic DNA contamination (eubacterial: human genomic DNA marker genes = 227.9:1) in the human feces. The newly-developed method robustly performs for fresh as well as stored fecal samples as demonstrated by 16S rRNA gene sequencing using 454 FLX+. Moreover, 16S rRNA gene analysis indicated that compared to other DNA extraction methods tested, the fecal metagenomic DNA isolated with current methodology retains species richness and does not show microbial diversity biases, which is further confirmed by qPCR with a known quantity of spike-in genomes. Overall, our data highlight a protocol with a balance between quality, amount, user-friendliness, and cost effectiveness for its suitability toward usage for culture-independent analysis of the human gut microbiome, which provides a robust solution to overcome key issues associated with fecal metagenomic DNA isolation in human gut microbiome studies.

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Unravelling the effects of the environment and host genotype on the gut microbiome

Cited by 1,318 publications

References 119 publications

Gastrointestinal microorganisms in cats and dogs: a brief review

Gastrointestinal microorganisms in cats and dogs: a brief review

Host genetic and environmental effects on mouse intestinal microbiota

An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

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