Inter-individual differences in the gene content of human gut bacterial species

Abstract

BackgroundGene content differences in human gut microbes can lead to inter-individual phenotypic variations such as digestive capacity. It is unclear whether gene content variation is caused by differences in microbial species composition or by the presence of different strains of the same species; the extent of gene content variation in the latter is unknown. Unlike pan-genome studies of cultivable strains, the use of metagenomic data can provide an unbiased view of structural variation of gut bacterial strains by measuring them in their natural habitats, the gut of each individual in this case, representing native boundaries between gut bacterial populations. We analyzed publicly available metagenomic data from fecal samples to characterize inter-individual variation in gut bacterial species.ResultsA comparison of 11 abundant gut bacterial species showed that the gene content of strains from the same species differed, on average, by 13% between individuals. This number is based on gene deletions only and represents a lower limit, yet the variation is already in a similar range as observed between completely sequenced strains of cultivable species. We show that accessory genes that differ considerably between individuals can encode important functions, such as polysaccharide utilization and capsular polysaccharide synthesis loci.ConclusionMetagenomics can yield insights into gene content variation of strains in complex communities, which cannot be predicted by phylogenetic marker genes alone. The large degree of inter-individual variability in gene content implies that strain resolution must be considered in order to fully assess the functional potential of an individual's human gut microbiome.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0646-9) contains supplementary material, which is available to authorized users.

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

“…In contrast, four of the discriminant genes were not detectable in the outlier persister with high levels of native B. longum (subject D). This analysis suggests interindividual variability of genes among the resident B. longum population, consistent with recent findings in several dominant species present in the human gut (Zhu et al, 2015).…”

“…However, B. longum levels did not explain the findings in all subjects, in that some persisters had relatively high levels of B. longum. Because traits that define niches and competitive interactions are not necessarily phylogenetically conserved in bacteria, and can differ substantially within the same bacterial species (Zhu et al, 2015), we used WMS data and compared the abundance of genes identified to belong to the species B. longum, at pretreatment baseline between persisters and non-persisters. A Wilcoxon test resulted in 70 genes with differential abundance between persisters and non-persisters ( Figure 3F; Table S4).…”

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

“…However, different strains of the same species can differ significantly in their gene content (Greenblum et al 2015;Zhu et al 2015) and single-nucleotide polymorphisms (SNPs) (Schloissnig et al 2013;Kashtan et al 2014;Lieberman et al 2014). These strain-level differences are important for understanding microbial evolution, adaptation, pathogenicity, and transmission.…”

Probióticos associados ao tratamento das doenças periodontais: revisão de literatura

“…Estudos recentes buscam o mapeamento desse microbioma, para, de forma unificada e específica, centrar ações terapêuticas cada vez mais na especificidade das lesões e doenças, evitando resistência microbiana, sobretratamentos, superdoses medicamentosas e utilização de medicamentos pouco ativos ou inativos para dada patologia 3 . Os probióticos estão no centro dessas descobertas, sendo os principais vetores para promoção de ação nos diferentes microrganismos endógenos humanos, visando ao desenvolvimento do processo de saúde no hospedeiro 4,5 . Esses agentes, que podem estar presentes em alimentos e também em alguns produtos específicos, têm sido utilizados em benefício da saúde e, em alguns casos, no tratamento adjuvante de algumas doenças.…”