Cultivation and description of Duncaniella dubosii sp. nov., Duncaniella freteri sp. nov. and emended description of the species Duncaniella muris

Miyake, Sou; Ding, Yichen; Soh, Melissa; Low, Adrian; Seedorf, Henning

doi:10.1099/ijsem.0.004137

Cited by 29 publications

(19 citation statements)

References 25 publications

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“…Of the Bacteroidota, the family Muribaculaceae have only been described recently, and few isolates have been obtained thus far [ 7 , 29 , 30 , 31 , 32 , 33 ]. Muribaculaceae were strongly impacted by WD, and this study is, to our knowledge, the first to analyze the relative abundance of Muribaculaceae ASVs in the different segments of the intestinal tract.…”

Section: Resultsmentioning

confidence: 99%

“…ASVs featured in heatmaps and ANCOM analyses were further annotated by taking the top BLASTn hit against the NCBI 16S rRNA gene database [ 17 ]. Phylogenetic lineages of Muribaculaceae and Lactobacilli were manually curated to identify recently recognized bacterial species or formal changes to nomenclature [ 7 , 30 , 31 , 33 , 56 ]. The “qiime emperor plot” command was used to generate custom PCoA plots of dissimilarity matrices with categorical groups on the x-axis against the first principal coordinate (PC1) on the y-axis and PC2 on the z-axis.…”

Section: Methodsmentioning

confidence: 99%

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Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract

Low

Soh

Miyake

et al. 2021

IJMS

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Dietary changes are known to alter the composition of the gut microbiome. However, it is less understood how repeatable and reversible these changes are and how diet switches affect the microbiota in the various segments of the gastrointestinal tract. Here, a treatment group of conventionally raised laboratory mice is subjected to two periods of western diet (WD) interrupted by a period of standard diet (SD) of the same duration. Beta-diversity analyses show that diet-induced microbiota changes are largely reversible (q = 0.1501; PERMANOVA, weighted-UniFrac comparison of the treatment-SD group to the control-SD group) and repeatable (q = 0.032; PERMANOVA, weighted-UniFrac comparison of both WD treatments). Furthermore, we report that diet switches alter the gut microbiota composition along the length of the intestinal tract in a segment-specific manner, leading to gut segment-specific Firmicutes/Bacteroidota ratios. We identified prevalent and distinct Amplicon Sequencing Variants (ASVs), particularly in genera of the recently described Muribaculaceae, along the gut as well as ASVs that are differentially abundant between segments of treatment and control groups. Overall, this study provides insights into the reversibility of diet-induced microbiota changes and highlights the importance of expanding sampling efforts beyond the collections of fecal samples to characterize diet-dependent and segment-specific microbiome differences.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract

Low

Soh

Miyake

et al. 2021

IJMS

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“…Bacteria classified in the family Muribaculaceae are abundant in the murine gut microbiome (20). While these bacteria are also found in humans (although at lower abundance), only a few members of this clade have been cultivated and described (21–23). As a result, the ecological roles of these bacteria have not yet been characterized, limiting the value of the mouse as a model system.…”

Section: Discussionmentioning

confidence: 99%

Muribaculaceae genomes assembled from metagenomes suggest genetic drivers of differential response to acarbose treatment in mice

Smith¹,

Miller

Schmidt

2020

Preprint

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AbstractThe drug acarbose (ACA) is used to treat diabetes, and by inhibiting alpha-amylase in the small intestine increases the amount of starch entering the lower digestive tract. This results in changes to the composition of the microbiota and its fermentation products. Acarbose also increases longevity in mice, an effect that could be related to increased production of the short-chain fatty acids propionate and butyrate. In experiments replicated across three study sites, two distantly related species in the bacterial family Muribaculaceae were dramatically more abundant in ACA treated mice, distinguishing these responders from other members of the family. Members of the Muribaculaceae likely produce propionate and are abundant and diverse in the guts of mice, although few isolates are available. We reconstructed genomes from metagenomes (MAGs) for eight populations of Muribaculaceae to examine what distinguishes species that respond positively to acarbose. We found two closely related MAGs (B1-A and B1-B) from one responsive species that both contain a polysaccharide utilization locus with a predicted extracellular alpha-amylase. These also shared a periplasmic neopullulanase with another, distantly related MAG (B2) representative of the only other responsive species. This gene differentiated these three MAGs from MAGs representative of non-responding species. Differential gene content in B1-A and B1-B may be associated with the inconsistent response of this species to acarbose across study sites. This work demonstrates the utility of culture-free genomics for inferring the ecological roles of gut bacteria including their response to pharmaceutical perturbations.ImportanceThe drug acarbose is used to treat diabetes by preventing the breakdown of starch in the small intestine, resulting in dramatic changes in the abundance of some members of the gut microbiome and its fermentation products. In mice, several of the bacteria that respond most positively are classified in the family Muribaculaceae, members of which produce propionate as a primary fermentation product. Propionate has been associated with gut health and increased longevity in mice. We found that genomes of the most responsive Muribaculaceae showed signs of specialization for starch fermentation, presumably providing them a competitive advantage in the large intestine of animals consuming acarbose. Comparisons among genomes support existing models for the ecological niches occupied by members of this family. In addition, genes encoding one type of enzyme known to participate in starch breakdown were found in all three genomes from responding species, but none of the others.

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“…Duncaniella muris (zOTU 8 with 99.5% similarity) is described to digest complex plant polysaccharides like hemicelluloses and pectins [57]. zOTU 12 was identified with 99.8% similarity as Duncaniella dubosii [58] and could be linked to the Candidatus Homeothermaceae strain H5 [59], which is part of the plant polysaccharide guild as well [57]. zOTU 26 has a 99.3% similarity to isolate-110 (HZI) [57] and is described as belonging to the plant polysaccharide guild.…”

Section: Discussionmentioning

confidence: 99%

Processing Matters in Nutrient-Matched Laboratory Diets for Mice—Microbiome

Wenderlein¹,

Böswald²,

Ulrich³

et al. 2021

Animals

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The composition of the microbiome is subject to the host’s diet. In commercial laboratory mouse diets, different physical forms of the same diets are available, containing—according to their labels—identical ingredients and nutrient compositions. However, variations in nutrient composition and starch gelatinization due to production processes and their impact on digestibility have been described. In this study, a total of 48 C57BL/J6 mice were assigned to two equal groups and were fed diets (produced with different processes—extruded vs. pelleted) for eight weeks in two biological replicates. At the end of the experiment, samples were collected from five different gastrointestinal regions, including the stomach, small intestine, cecum, large intestine, and an extracorporeal region (feces), and the microbiome was analyzed with 16S rRNA gene amplicon sequencing. The replicates in both experiments differed significantly in their relative abundances of Muribaculaceae species. Furthermore, the gastrointestinal content of pellet-fed mice contained larger numbers of Lactobacillus species. These results indicate that starch gelatinization and ingredient composition significantly influence microbial makeup. In conclusion, different feed processing methods may affect fundamental digestive and metabolic processes, impacting animal experiments and biasing microbiome data.

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Cultivation and description of Duncaniella dubosii sp. nov., Duncaniella freteri sp. nov. and emended description of the species Duncaniella muris

Abstract: Three bacterial strains, C9, H5 and TLL-A3, were isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of 16S rRNA genes indicated that the strains belonged to the Muribaculaceae … Show more

Cited by 29 publications

References 25 publications

Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract

Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract

Muribaculaceae genomes assembled from metagenomes suggest genetic drivers of differential response to acarbose treatment in mice

Processing Matters in Nutrient-Matched Laboratory Diets for Mice—Microbiome

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