Taxonogenomic description of four new Clostridium species isolated from human gut: ‘Clostridium amazonitimonense’ , ‘Clostridium merdae’ , ‘Clostridium massilidielmoense’ and ‘Clostridium nigeriense’

Alou, Maryam Tidjani; Ndongo, S.; Frégère, L.; Labas, N.; Andrieu, Claudia; Richez, Magali; Couderc, Carine; Baudoin, Jean-Pierre; Abrahão, Jônatas Santos; Brah, Souleymane; Diallo, Aldiouma; Sokhna, C.; Cassir, Nadim; Scola, Bernard La; Cadoret, F.; Raoult, Didier

doi:10.1016/j.nmni.2017.11.003

Cited by 27 publications

(16 citation statements)

References 38 publications

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“…A new species was defined by a 16S rRNA gene sequence homology below 98.65% with that of the phylogenetically closest neighbor validated in standing nomenclature (Stackebrandt, 2006;Meier-Kolthoff et al, 2013). The genomes of these taxa were then sequenced as previously described (Alou et al, 2018).…”

Section: Culturomicsmentioning

confidence: 99%

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut

et al. 2020

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Human urine was considered sterile for a long time. However, 416 species have been previously cultured, including only 40 anaerobic species. Here, we used culturomics, particularly those targeting anaerobes, to better understand the urinary microbiota. By testing 435 urine samples, we isolated 450 different bacterial species, including 256 never described in urine of which 18 were new species. Among the bacterial species identified, 161 were anaerobes (35%). This study increased the known urine repertoire by 39%. Among the 672 bacterial species isolated now at least once from urine microbiota, 431 (64.1%) were previously isolated from gut microbiota, while only 213 (31.7%) were previously isolated from vagina. These results suggest that many members of the microbiota in the urinary tract are in fact derived from the gut, and a paradigm shift is thus needed in our understanding.

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Section: Culturomicsmentioning

confidence: 99%

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut

et al. 2020

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“…Dechloromonas and Saccharibacteria are often found in activated sludge [ 68 , 74 , 75 ]; some representatives of Saccharibacteria phylum are able to decompose toluene [ 76 ]. Clostridium species are strictly anaerobic bacteria that can metabolize various compounds, such as carbohydrates, amino acids, alcohols, amino acids or purines [ 77 ]. Thus, microbial communities of different functional zones within a CW were completely different from the microbiomes (Caldilinea, Opitutus, and Prosthecobacter among dominant genera) of activated sludge obtained from wastewater treatment plants in the Moscow region [ 78 ].…”

Section: Discussionmentioning

confidence: 99%

Spatial Changes in Microbial Communities along Different Functional Zones of a Free-Water Surface Wetland

et al. 2020

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Constructed wetlands (CWs) are complicated ecosystems that include vegetation, sediments, and the associated microbiome mediating numerous processes in wastewater treatment. CWs have various functional zones where contrasting biochemical processes occur. Since these zones are characterized by different particle-size composition, physicochemical conditions, and vegetation, one can expect the presence of distinct microbiomes across different CW zones. Here, we investigated spatial changes in microbiomes along different functional zones of a free-water surface wetland located in Moscow, Russia. The microbiome structure was analyzed using Illumina MiSeq amplicon sequencing. We also determined particle diameter and surface area of sediments, as well as chemical composition of organic pollutants in different CW zones. Specific organic particle aggregates similar to activated sludge flocs were identified in the sediments. The highest accumulation of hydrocarbons was found in the zones with predominant sedimentation of fine fractions. Phytofilters had the highest rate of organic pollutants decomposition and predominance of Smithella, Ignavibacterium, and Methanothrix. The sedimentation tank had lower microbial diversity, and higher relative abundances of Parcubacteria, Proteiniclasticum, and Macellibacteroides, as well as higher predicted abundances of genes related to methanogenesis and methanotrophy. Thus, spatial changes in microbiomes of constructed wetlands can be associated with different types of wastewater treatment processes.

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“…Some studies have proposed that Mycoplasmas are commensal gut or even intra-host dependent microorganisms in Atlantic salmon [29], [95]. Gemmatimonadetes are largely uncharacterised though have been found previously in the gut of sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax), at low abundances [96]. Clostridiaceae (Clostridium sensu stricto) are common gut bacteria and are metabolically flexible, capable of metabolising a range of carbohydrates to produce alcohols and acids [97].…”

Section: Discussionmentioning

confidence: 99%

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae

Keating

Bolton‐Warberg

Hinchcliffe

et al. 2020

Preprint

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Background: Aquaculture successfully meets global food demands for many fish species. However, squaculture production of Atlantic cod (Gadus morhua) is modest in comparison to market demand. For cod farming to be a viable economic venture specific challenges on how to increase growth, health and farming productivity need to be addressed. Feed ingredients play a key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with both health and economic benefits for terrestrial farmed animals and fish. The impact of such dietary supplements to cod gut integrity and microbiota, which contribute to overall fish robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic cod with macroalgae and determine the impacts on fish condition and growth, gut morphology and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack (Ascophyllum nodosum) or sea lettuce (Ulva rigida) macroalgae in a 12-week trial. Results: The results demonstrated that there was no significant difference in fish condition, gut morphology or hindgut microbiota between the U. rigida supplemented fish group and the control group at any time point. This contrasts with the A. nodosum treatment. Fish within this group were further categorised as either 'Normal' or 'Lower Growth'. 'Lower Growth' individuals found the diet unpalatable resulting in reduced weight and condition factor combined with an altered gut morphology and microbiome relative to the other treatments. Excluding this group, our results show that the hindgut microbiota were largely driven by temporal pressures with the microbial communities becoming more similar over time irrespective of dietary treatment. The core microbiome at the final time-point consisted of the orders Vibrionales (Vibrio and Photobacterium), Bacetroidales (Bacetroidetes and Macellibacteroides) and Clostridiales (Lachnoclostridium. Conclusions: Our study indicates that U. rigida macroalgae can be supplemented at 10% inclusion levels in the diet of jevenile farmed Atlantic cod without any impact on fish condition or hindgut microbial community structure. We also conclude that 10% dietary inclusion of A. nodosum is not a suitable feed supplement in a farmed cod diet.

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Taxonogenomic description of four new Clostridium species isolated from human gut: ‘Clostridium amazonitimonense’ , ‘Clostridium merdae’ , ‘Clostridium massilidielmoense’ and ‘Clostridium nigeriense’

Cited by 27 publications

References 38 publications

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut

Spatial Changes in Microbial Communities along Different Functional Zones of a Free-Water Surface Wetland

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae

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