Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes

Marchandin, Hélène; Teyssier, Corinne; Campos, Josiane; Jean-Pierre, Hélène; Roger, Frédéric; Carlier, Jean‐Philippe; Jumas‐Bilak, Estelle

doi:10.1099/ijs.0.013102-0

Cited by 144 publications

(117 citation statements)

References 32 publications

(42 reference statements)

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“…Three different biochemical pathways for propionate production are known to be present in the microbiota (Figure 1). Bacteroidetes utilise the succinate pathway via methylmalonyl-CoA (Macy and Probst, 1979), which is also present in several Firmicutes bacteria belonging to the recently proposed new class of Negativicutes (formerly classed as Veillonellaceae or Clostridial cluster IX (Marchandin et al, 2010)). Bacteroidetes mainly utilise polysaccharides and peptides for growth (Macy andProbst, 1979, Flint et al, 2012a), whereas in Firmicutes propionate formation has been reported from organic acids as well (Seeliger et al, 2002;Watanabe et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

et al. 2014

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Propionate is produced in the human large intestine by microbial fermentation and may help maintain human health. We have examined the distribution of three different pathways used by bacteria for propionate formation using genomic and metagenomic analysis of the human gut microbiota and by designing degenerate primer sets for the detection of diagnostic genes for these pathways. Degenerate primers for the acrylate pathway (detecting the lcdA gene, encoding lactoylCoA dehydratase) together with metagenomic mining revealed that this pathway is restricted to only a few human colonic species within the Lachnospiraceae and Negativicutes. The operation of this pathway for lactate utilisation in Coprococcus catus (Lachnospiraceae) was confirmed using stable isotope labelling. The propanediol pathway that processes deoxy sugars such as fucose and rhamnose was more abundant within the Lachnospiraceae (based on the pduP gene, which encodes propionaldehyde dehydrogenase), occurring in relatives of Ruminococcus obeum and in Roseburia inulinivorans. The dominant source of propionate from hexose sugars, however, was concluded to be the succinate pathway, as indicated by the widespread distribution of the mmdA gene that encodes methylmalonyl-CoA decarboxylase in the Bacteroidetes and in many Negativicutes. In general, the capacity to produce propionate or butyrate from hexose sugars resided in different species, although two species of Lachnospiraceae (C. catus and R. inulinivorans) are now known to be able to switch from butyrate to propionate production on different substrates. A better understanding of the microbial ecology of short-chain fatty acid formation may allow modulation of propionate formation by the human gut microbiota.

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Section: Introductionmentioning

confidence: 99%

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

et al. 2014

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“…However, this species showed positive reactions for several glycoside hydrolases showing potential for carbohydrate degradation. Negativicoccus succinicivorans is a novel little studied bacterium; however, succinate has been shown to support the growth of this bacterium [37]. Succinate can be produced by several gut bacteria such as Bacteroides species.…”

Section: Discussionmentioning

confidence: 99%

Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate

Adamberg

2018

Microbial Ecology in Health and Disease

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Background: Nutrient and energy metabolism in human colon depends on bacterial growth rate that is determined by the colonic transit rate.Objective: A novel approach, De-stat culture was used to distinguish the fast and slow growing sub-populations from fecal microbiota.Design: The enrichment and metabolism of bacteria from pooled fecal cultures of children was studied at dilution rates D = 0.2–0.0 1/h in mucin-supplemented media containing either arabinogalactan or apple pectin.Results: The study revealed clear differentiation of the fecal microbiota at higher (above 0.1 1/h) and lower (below 0.1 1/h) dilution rates, along with metabolic changes. Similarity of the fast and slow growing bacteria was observed in two different fecal pools and on both substrates, suggesting the dilution rate as the main triggering parameter for selection of bacteria. At high dilution rates, the species Collinsella aerofaciens, Dorea longicatena, Escherichia coli, Lachnoclostridium torques, and different Bacteroides (B. caccae, B. fragilis, B. ovatus, B. thetaiotaomicron, B. vulgatus) were dominant in both media variants. At low dilution rates, Akkermansia muciniphila, Eisenbergiella tayi, Negativicoccus succinivorans, and a group of Ruminococcaceae became dominant in both media and in both fecal pools. This change in bacterial population accompanied by the increased production of propionic and butyric acids as well as higher consumption of alanine and branched chain amino acids at low dilution rates.Conclusions: The study suggests that specific growth rate has important effect on the dynamics of colon microbiota. Manipulation of the proportions of fast and slow growing gut bacteria through modulation of the transit rate could be a target in human nutrition studies. The De-stat study would enable to predict changes in microbiota composition associated with the decrease or increase of the colonic transit rate.

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“…Alignment of the complete 16S rRNA sequence from our clinical bacteremia isolate and three nearly complete 16S rRNA sequences from the Negativicoccus type strain using ClustalW2 (http://www.ebi.ac.uk/Tools /clustalw2/index.html) also showed almost complete identity (99.9%) of these sequences. Phylogenetic analysis using MEGA 4.0 software (12) and the neighbor-joining method also showed high bootstrap scores between our blood isolate and the sequences from the Negativicoccus type strain (8), while other genera in the family Veillonellaceae, Veillonella and Dialister in particular, were closely related but had lower bootstrap scores (Fig. 1).…”

Section: Case Reportmentioning

confidence: 99%

“…However, a recent BLAST search (July 2010) of the clinical sequence using both the GenBank and IDNS databases demonstrated references with 100% identity. The references were to a recently described species, Negativicoccus succinicivorans (type strain ADV 07/08/06-B-1388 T ), within the Veillonellaceae family in the phylum Firmicutes that was recently isolated from human skin and soft tissue samples and described using phenotypic and genetic methods (8). Matching of the complete 16S rRNA gene sequence (ϳ1,527 bp) from our clinical bacteremia isolate to the nearly complete reference sequences (ϳ1,401 bp) from the skin and soft tissue Negativicoccus type strain from GenBank (accession numbers FJ715928, FJ715929, and FJ715930) using both the GenBank and the IDNS databases showed them to be highly (Ͼ99%) similar.…”

Section: Case Reportmentioning

confidence: 99%

Identification by 16S rRNA Gene Sequencing of Negativicoccus succinicivorans Recovered from the Blood of a Patient with Hemochromatosis and Pancreatitis

Church¹,

Simmon²,

Sporina³

et al. 2011

J Clin Microbiol

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We describe a case of Negativicoccus succinicivorans bacteremia in an adult man with hemochromatosis and acute pancreatitis. Conventional phenotypic tests and commercial identification systems failed to definitively identify the tiny anaerobic Gram-negative coccus isolated from two sets of blood cultures. The bacterium was identified by 16S rRNA gene sequencing and analysis using the SmartGene Integrated Database Network System software. This is the first published report of the recovery of this organism from a patient with invasive infection. CASE REPORTA 57-year-old man with hemochromatosis was admitted to the hospital in June 2008 with acute pancreatitis. He had a history of chronic alcohol abuse. He complained of abdominal pain and diarrhea. The physical examination revealed a temperature of 38.4°C and lower abdominal tenderness without rebound tenderness. Computerized tomography scanning revealed peripancreatic inflammation consistent with pancreatitis. A complete blood count and differential showed anemia (hemoglobulin ϭ 118 g/liter), thrombocytopenia (68 ϫ 10 9 cells/ml), and a normal white blood cell count (6.9 ϫ 10 9 cells/ml), with a normal level of polymorphonuclear cells but a low level of lymphocytes. He had mild renal dysfunction, with a serum creatinine level of 111 g/liter. Pancreatitis was confirmed, and he had an increasingly elevated lipase level (from 225 to 978 IU), documented within the initial 48 h in the hospital, and associated mild hepatocellular dysfunction with an elevated gamma-glutamyl transferase level (587 g/liter). The total bilirubin was also mildly increased at 16 g/liter. Stool tests were negative for Clostridium difficile toxins (A and B), Salmonella, Shigella, Campylobacter, Escherichia coli O157, Aeromonas, and Plesiomonas, and a Giardia/Cryptosporidium enzyme immunoassay (EIA) was negative.Two sets of blood samples were collected and cultured with BacT/Alert blood culture system (bioMérieux Canada, Laval, Quebec, Canada) FA (aerobic) and FN (anaerobic) bottles, and the FN bottles in both sets were positive, as described below. Supportive therapy included administration of antibiotics (one dose of cefuroxime and then piperacillin-tazobactam), and the patient recovered uneventfully after 4 days of hospitalization and was discharged.

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Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes

Cited by 144 publications

References 32 publications

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate

Identification by 16S rRNA Gene Sequencing of Negativicoccus succinicivorans Recovered from the Blood of a Patient with Hemochromatosis and Pancreatitis

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