Genomic Analysis of a Pathogenic Bacterium, Paeniclostridium sordellii CBA7122 Containing the Highest Number of rRNA Operons, Isolated from a Human Stool Sample

Kim, Joon Yong; Kim, Yeon Bee; Song, Hye Seon; Chung, Won‐Hyong; Lee, Changsu; Ahn, Seung Woo; Lee, Se Hee; Jung, Min Young; Kim, Tae-Woon; Nam, Young-Do; Roh, Seong Woon

doi:10.3389/fphar.2017.00840

Cited by 17 publications

(12 citation statements)

References 17 publications

(16 reference statements)

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“…In this study, 12 differential OTUs including one class, one order, three families, and seven genera are obtained. Paeniclostridium is considered a potential pathogen, it may be related to soft tissue infection and toxic shock (Kim et al 2017 ). Gelria ( Thermoanaerobacterales Order, Thermoanaerobacteraceae Family) is known to be related to the metabolism of VFAs (FitzGerald et al 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Effect of Broussonetia papyrifera silage on the serum indicators, hindgut parameters and fecal bacterial community of Holstein heifers

et al. 2020

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This study investigated the effects of substitution of whole corn silage (WCS) with Broussonetia papyrifera silage (BPS) in different ratios on the serum indicators, hindgut fermentation parameters (pH, ammoniacal nitrogen, and volatile fatty acids), and fecal bacterial community of Holstein heifers. Sixteen heifers (8-month-old, 220 ± 30 kg) were randomly divided into four treatments according to different BPS substitution ratios of feed basis (0%, 25%, 50%, and 75%). The experiment consisted of a 7-day preliminary feeding period and a 30-day experimental period. On the last day of the trial, the blood samples were collected from caudal vein, and the feces samples were collected from rectum. With the increasing of BPS content, the concentration of malondialdehyde (MDA) and interleukin-1β (IL-1β) in serum decreased (P < 0.05), and the immunoglobulin A (IgA) and IL-4 content of serum increased (P < 0.05); and the hindgut pH value increased (P < 0.05). 16S rRNA sequencing found that the dominant phyla were Firmicutes, Bacteroidetes, and Verrucomicrobia; and the dominant genera were Ruminococcaceae_UCG-005, Ruminococcaceae_UCG-010, and Rikenellaceae_RC9_gut_group. Linear Discriminant Analysis Effect Size (LEfSe) analysis found 12 differential operational taxonomic units (OTUs) which have strong correlation with some serum and hindgut indicators, and have the potential to be used as biomarkers. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) found that BPS have impacts on the pathways, such as carbohydrate transport and metabolism, and promotes amino acid transport and metabolism. To sum up, inclusion of BPS in heifer diets can affect serum anti-oxidant and immune indicators, fecal parameters, composition and function of fecal microorganisms in Holstein heifers.

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Section: Discussionmentioning

confidence: 99%

Effect of Broussonetia papyrifera silage on the serum indicators, hindgut parameters and fecal bacterial community of Holstein heifers

et al. 2020

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“…And yet, the rRNA locus represents a notably dynamic region of the genome [22][23][24][25] that exhibits wide intraspecific variation in copy number. Intraspecific variation in rDNA copy number is not widely reported in studies of prokaryotes [14], although some bacteria tolerate a change in rDNA copy number [31][32][33] such as an expansion to 17 rDNA copies in the genome of Paeniclostridium sordellii CBA7122, whose genome usually contains an average of four 16S rDNA copies [34]. In eukaryotes, by contrast, substantial intraspecific variation in rDNA copy number appears commonplace [24,25].…”

Section: Intraspecific Variation In Rdna Copy Number In Prokaryotes and Eukaryotesmentioning

confidence: 99%

Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?

Lavrinienko

Jernfors

Koskimäki

et al. 2021

Trends in Microbiology

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“…The number and location of rRNA operons ( rrn ) is very diverse: they may be present in 1–15 copies in prokaryotic genomes ( Schmidt, 1997 ; Klappenbach et al, 2001 ; Pei et al, 2010 ) and over 80% bacterial genomes sequenced have more than one operon. Recently, the presence of 17 rrs was reported in Paeniclostridium sordellii CBA7122, a species with genomes containing 1 to 8 rRNA operons ( Kim et al, 2017 ). Figure 1 shows the median of the number of rrs copies in 3,070 bacterial species according to data reported in rrn DB database ( Stoddard et al, 2015 ; Supplementary Table S1 show the data in detail).…”

Section: Ribosomal Rna Operons In Bacteriamentioning

confidence: 99%

Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evolution and Potential Consequences on the Rate of Evolution of Their 16S rRNA

Espejo

Plaza

2018

Front. Microbiol.

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Bacterial species differ greatly in the number and location of the rRNA operons which may be present in the bacterial chromosomes and plasmids. Most bacterial species contain more than one ribosomal RNA operon copy in their genomes, with some species containing up to 15 such copies. We review the number and location of the rRNA operons and discuss evolution of 16S rRNA (rrs) genes -which are considered as ultimate chronometers for phylogenetic classification- in bacteria with multiple copies of these genes. In these bacterial species, the rrs genes must evolve in concert and sequence changes generated by mutation or horizontal gene transfer must be either erased or spread to every gene copy to avoid divergence, as it occurs when they are present in different species. Analysis of polymorphic sites in intra-genomic rrs copies identifies putative conversion events and demonstrates that sequence conversion is patchy and occurs in small conversion tracts. Sequence conversion probably arises by a non-reciprocal transfer between two or more copies where one copy contributes only a small contiguous segment of DNA, whereas the other copy contributes the rest of the genome in a fairly well understood molecular process. Because concerted evolution implies that a mutation in any of the rrs copies is either eliminated or transferred to every rrs gene in the genome, this process should slow their evolution rate relative to that of single copy genes. However, available data on the rrs genes in bacterial genomes do not show a clear relationship between their evolution rates and the number of their copies in the genome.

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Genomic Analysis of a Pathogenic Bacterium, Paeniclostridium sordellii CBA7122 Containing the Highest Number of rRNA Operons, Isolated from a Human Stool Sample

Cited by 17 publications

References 17 publications

Effect of Broussonetia papyrifera silage on the serum indicators, hindgut parameters and fecal bacterial community of Holstein heifers

Effect of Broussonetia papyrifera silage on the serum indicators, hindgut parameters and fecal bacterial community of Holstein heifers

Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?

Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evolution and Potential Consequences on the Rate of Evolution of Their 16S rRNA

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