Genomic and functional analysis ofRomboutsia ilealisCRIB^Treveals adaptation to the small intestine

Abstract

BackgroundThe microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host.MethodsThe genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC.ResultsWe present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides.DiscussionThis revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.

Development of the Ileal Microbiota in Three Broiler Breeds

“…Four of six ASVs assigned to Romboutsia were differentially abundant in the lumen, presenting a stronger case for a true biological preference for lumen colonization. Under laboratory conditions, Romboutsia is unable to grow on mucin which is likely to due its inability to degrade mucus derived carbohydrates such as L-fucose and sialic acid (51). This experimental data supports the finding that Romboutsia was differentially abundant in the lumen and may have a higher absolute abundance in the lumen.…”

“…The presence of Clostridioides difficile in the chicken ileum has been reported and discussed with respect to public health (50) but no studies mention the impact of this species on poultry health. Genomic and functional analysis of Romboutsia found in the human gastrointestinal tract reveal that these Clostridia are highly adapted to life in the small intestine with the ability to ferment glucose and other simple carbohydrates (51). Secondly, Erysipelotrichaceae was found in the ileum from 21 d.p.h in this study.…”

Identification microflora related to growth performance in pigs based on 16s rRNA sequence analyses

“…This conclusion is consistent in the two experiments of this study. The OTUs associated with Streptococcus were associated with lactic acid-producing bacteria, and Escherichia-Shigella and Romboutsia are associated with glucose degradation and absorption (Delgado-Andrade et al, 2017;Gerritsen et al, 2017). This conclusion is similar to the results of this study and to some extent supports the results of this study.…”

“…Previous studies revealed that many species of Escherichia-Shigella and Romboutsia, which are most abundant in the intestinal tract, contribute to the degradation of glucose and fructooligosaccharides (Delgado-Andrade et al, 2017;Gerritsen et al, 2017). In this study, these two bacteria groups were also found to be signi cantly different in the intestines of Duroc and Landrace pigs, but there was no signi cant difference in the contents of Escherichia-shigella and Romboutsia in the intestines of Yorkshire pigs with different growth performance.…”

Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer

“…Moreover, Romboutsia taxa is the genus with the highest relative abundance in HMT vs. CMP samples. Notably, Romboutsia is a recently described bacterial genus 48 , 49 commonly identified in the human gut 50 , 51 , and often associated with a healthy status of patients 50 , 51 . The drastic reduction of members of this particular genus (−86,51%) in mucosa associated with polyps may represent a potential microbial indicator of a disease condition 50 .…”