Genomic variation landscape of the human gut microbiome

By S. Schloissnig, Manimozhiyan Arumugam, Shinichi Sunagawa, M. Mitreva, Julien Tap, Ana Zhu, Alison S. Waller, Daniel R. Mende, Jens Roat Kultima, John Martin and 4 more. Nature, 2012

855 citations recorded by the source corpus.

Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1c4e966ad58ce2c456a1f96b2902594eeefdfd6e

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Citations in the corpus

The Central Nervous System and the Gut Microbiome (2016, background): “Importantly, the healthy microbiome is temporally stable, even when subjected to recurrent mild disturbances (Dethlefsen et al., 2008; Oh et al., 2016; Schloissnig et al., 2013).”
Antibiotic-Induced Changes in the Intestinal Microbiota and Disease. (2016, background): “In fact, clindamycin resistance transfer factor gene (btgA) has been identified as carrying the highest number of singlenucleotide polymorphisms (SNPs) within 200 human gut metagenomes, and other conjugal transfer factors have followed in this ranking [112].”
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome (2018, background): “Because considerable individualized strain-level heterogeneity has been observed in the human microbiome (Franzosa et al., 2015; Schloissnig et al., 2013; Truong et al., 2017), finding the same strain in the mother and in the infant would give strong evidence of intra-pair transmission.”
Microbial strain-level population structure and genetic diversity from metagenomes (2017, positive): “One of the key biological observations of this study is that only one strain typically dominates each species in the human gut, and retention of this individualized dominant strain over time helps to explain the previously reported stability of the gut microbiome (Schloissnig et al. 2013; Franzosa e”
Antibiotics and the gut microbiota. (2014, neutral): “Interestingly, in a study of genomic variation in over 200 individuals, conjugative elements with resistance functions were found to have the highest SNP density of all annotatable genes (55).”
Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley (2015, background): “A high SNP density, indicative of positive selection, was also found for the CAS proteins csy1 and cse2 in metagenome samples of human gut microbiomes (Schloissnig et al., 2013).”
Microbial genes, brain & behaviour – epigenetic regulation of the gut–brain axis (2014, background): “…and a plethora of diverse micro-organisms now colonize virtually all body surfaces of animal hosts, residing as beneficial symbionts, harmless commensals or pathogenic parasites (Dave et al. 2012; Schloissnig et al. 2013; Turnbaugh et al. 2007) most prominently within the gastrointestinal tract.”
The Host Shapes the Gut Microbiota via Fecal microRNA (2016, neutral): “At approximately 3 years of age in humans, the intestinal microbiota resembles an adult-like microbiota that is relatively stable over time (Faith et al., 2013; Schloissnig et al., 2013).”
The healthy human microbiome (2016, background): “temporal stability than do microbial abundance profiles [8, 73, 74].”
eggNOG v4.0: nested orthology inference across 3686 organisms (2013, methodology): “The repository of >3496 prokaryotic genomes has been used for several large-scale prokaryotic genome and metagenome analyses (35), and is intended to accommodate new prokaryotic genomes as D232 Nucleic Acids Research, 2014, Vol.”