Functional Intestinal Metagenomics

Bogert, Bartholomeus van den; Leimena, Milkha M.; Vos, Willem M. de; Zoetendal, Erwin G.; Kleerebezem, Michiel

doi:10.1002/9781118010549.ch18

Cited by 12 publications

(11 citation statements)

References 111 publications

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“…Although the influence of oxygen cannot be ruled out, investigations in our laboratory revealed that the ileostoma effluent microbiota contain a high relative abundance of strict anaerobes (Booijink et al ., ). Moreover, the ileostoma effluent microbiota resemble that encountered in the proximal part of the small intestine of individuals with an normal intestinal tract that includes a colon (van den Bogert et al ., ; Zoetendal et al ., ). Streptococcus and Veillonella populations were detected in all ileostoma effluent samples and showed fluctuations in relative abundance in a 72‐h time frame, which are most likely due to the subject's diet composition.…”

Section: Discussionmentioning

confidence: 97%

“…The human body is populated with complex microbial communities, which vary in composition between body sites (Costello et al ., ). The microbiota in the human gastrointestinal (GI) tract, for example, have adapted to the different conditions in the specific GI habitats [for a recent review see (Walter & Ley, )] and are impressive not only because of its very high population density, but also because of its high phylogenetic diversity (Rajilić‐Stojanović et al ., ; van den Bogert et al ., ,b) and its extensive functional capabilities that complement the human genetic potential (Qin et al ., ). The composition and dynamics of the bacterial community in the lower GI tract have been well described (Booijink et al ., ; Rajilić‐Stojanović et al ., ; Tap et al ., ; Turnbaugh et al ., ), whereas the upper GI tract microbiota in healthy humans are less well characterized as a consequence of sampling difficulties (Booijink et al ., ; Leser & Molbak, ; Cotter, ).…”

Section: Introductionmentioning

confidence: 97%

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Diversity of human small intestinalStreptococcusandVeillonellapopulations

Bogert

Erkuş

Boekhorst³

et al. 2013

FEMS Microbiol Ecol

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139

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Molecular and cultivation approaches were employed to study the phylogenetic richness and temporal dynamics of Streptococcus and Veillonella populations in the small intestine. Microbial profiling of human small intestinal samples collected from four ileostomy subjects at four time points displayed abundant populations of Streptococcus spp. most affiliated with S. salivarius, S. thermophilus, and S. parasanguinis, as well as Veillonella spp. affiliated with V. atypica, V. parvula, V. dispar, and V. rogosae. Relative abundances varied per subject and time of sampling. Streptococcus and Veillonella isolates were cultured using selective media from ileostoma effluent samples collected at two time points from a single subject. The richness of the Streptococcus and Veillonella isolates was assessed at species and strain level by 16S rRNA gene sequencing and genetic fingerprinting, respectively. A total of 160 Streptococcus and 37 Veillonella isolates were obtained. Genetic fingerprinting differentiated seven Streptococcus lineages from ileostoma effluent, illustrating the strain richness within this ecosystem. The Veillonella isolates were represented by a single phylotype. Our study demonstrated that the small intestinal Streptococcus populations displayed considerable changes over time at the genetic lineage level because only representative strains of a single Streptococcus lineage could be cultivated from ileostoma effluent at both time points.

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Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 97%

Diversity of human small intestinalStreptococcusandVeillonellapopulations

Bogert

Erkuş

Boekhorst³

et al. 2013

FEMS Microbiol Ecol

Self Cite

139

110

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“…Carnivores, omnivores and herbivores could be distinguished by increasing microbiota diversity, which probably reflects the large variety of plant-derived carbohydrates in the diet of herbivores. The differences in composition and diversity of intestinal tract microbiota in these animal groups indicate that both diet and host collectively affect the microbial composition [ 11 – 13 ].…”

Section: Introductionmentioning

confidence: 99%

Mouse models for human intestinal microbiota research: a critical evaluation

Hugenholtz

Vos

2017

Cell. Mol. Life Sci.

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431

323

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Since the early days of the intestinal microbiota research, mouse models have been used frequently to study the interaction of microbes with their host. However, to translate the knowledge gained from mouse studies to a human situation, the major spatio-temporal similarities and differences between intestinal microbiota in mice and humans need to be considered. This is done here with specific attention for the comparative physiology of the intestinal tract, the effect of dietary patterns and differences in genetics. Detailed phylogenetic and metagenomic analysis showed that while many common genera are found in the human and murine intestine, these differ strongly in abundance and in total only 4% of the bacterial genes are found to share considerable identity. Moreover, a large variety of murine strains is available yet most of the microbiota research is performed in wild-type, inbred strains and their transgenic derivatives. It has become increasingly clear that the providers, rearing facilities and the genetic background of these mice have a significant impact on the microbial composition and this is illustrated with recent experimental data. This may affect the reproducibility of mouse microbiota studies and their conclusions. Hence, future studies should take these into account to truly show the effect of diet, genotype or environmental factors on the microbial composition.Electronic supplementary materialThe online version of this article (doi:10.1007/s00018-017-2693-8) contains supplementary material, which is available to authorized users.

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“…The microbial ecology of the human small intestine is of interest since it is the first site where intestinal microbes interact with ingested food components [1]. Due to poor physical accessibility, there is only limited knowledge of the microbial gene functions and metabolic pathways that are operating in the small intestine microbiota.…”

Section: Introductionmentioning

confidence: 99%

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

et al. 2013

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Background: Next generation sequencing (NGS) technologies can be applied in complex microbial ecosystems for metatranscriptome analysis by employing direct cDNA sequencing, which is known as RNA sequencing (RNA-seq). RNA-seq generates large datasets of great complexity, the comprehensive interpretation of which requires a reliable bioinformatic pipeline. In this study, we focus on the development of such a metatranscriptome pipeline, which we validate using Illumina RNA-seq datasets derived from the small intestine microbiota of two individuals with an ileostomy. Results: The metatranscriptome pipeline developed here enabled effective removal of rRNA derived sequences, followed by confident assignment of the predicted function and taxonomic origin of the mRNA reads. Phylogenetic analysis of the small intestine metatranscriptome datasets revealed a strong similarity with the community composition profiles obtained from 16S rDNA and rRNA pyrosequencing, indicating considerable congruency between community composition (rDNA), and the taxonomic distribution of overall (rRNA) and specific (mRNA) activity among its microbial members. Reproducibility of the metatranscriptome sequencing approach was established by independent duplicate experiments. In addition, comparison of metatranscriptome analysis employing single-or paired-end sequencing methods indicated that the latter approach does not provide improved functional or phylogenetic insights. Metatranscriptome functional-mapping allowed the analysis of global, and genus specific activity of the microbiota, and illustrated the potential of these approaches to unravel syntrophic interactions in microbial ecosystems. Conclusions: A reliable pipeline for metatransciptome data analysis was developed and evaluated using RNA-seq datasets obtained for the human small intestine microbiota. The set-up of the pipeline is very generic and can be applied for (bacterial) metatranscriptome analysis in any chosen niche.

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Functional Intestinal Metagenomics

Cited by 12 publications

References 111 publications

Diversity of human small intestinalStreptococcusandVeillonellapopulations

Diversity of human small intestinalStreptococcusandVeillonellapopulations

Mouse models for human intestinal microbiota research: a critical evaluation

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

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