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Yi SW, Lee HG, Kim E, Jung YH, Bok EY, Cho A, Do YJ, So KM, Hur TY, Oh SI. Gut microbiota alteration with growth performance, histopathological lesions, and immune responses in Salmonella Typhimurium-infected weaned piglets. Vet Anim Sci 2023; 22:100324. [PMID: 38125715 PMCID: PMC10730377 DOI: 10.1016/j.vas.2023.100324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Salmonella Typhimurium can cause gastroenteritis in weaned piglets, which are particularly vulnerable to dietary changes and dysfunction of their immature organs. The colonization of S. Typhimurium could disrupt the gut microbiota and increase susceptibility to the bacterium. This study aimed to investigate the alterations of gut microbiota in S. Typhimurium-infected weaned piglets. Ten 49-day-old pigs were divided into two groups: S. Typhimurium-inoculated (ST, n = 6) and negative control (NC, n = 4) groups. The body weight and S. Typhimurium fecal shedding were monitored for 14 days after S. Typhimurium inoculation (dpi). The intestinal tissues were collected at 14 dpi; histopathological lesions and cytokine gene expression were evaluated. The gut microbiome composition and short-chain fatty acid concentrations were analyzed in fecal samples collected at 14 dpi. The average daily gain and gut microbiota alpha diversity in ST group tended to be lower than NC group at 14 dpi. Linear discriminant analysis effect size results showed a significant increase in the abundance of two genera and five species, while a significant decrease was observed in the five genera and nine species within the gut microbiota of ST group. Among the significantly less abundant bacteria in the ST group, Lachnospira eligens and Anaerobium acetethylicum produce acetate and butyrate, and may be considered as key S. Typhimurium infection-preventing bacteria. The overall results provide invaluable information about changes in the gut microbiota of S. Typhimurium-infected weaned piglets, which can be used to develop alternative measures to antibiotics and prevent ST bacterial infection.
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Affiliation(s)
- Seung-Won Yi
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju, Jeollabuk-do 55365, South Korea
| | - Han Gyu Lee
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju, Jeollabuk-do 55365, South Korea
| | - Eunju Kim
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju, Jeollabuk-do 55365, South Korea
| | - Young-Hun Jung
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju, Jeollabuk-do 55365, South Korea
| | - Eun-Yeong Bok
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju, Jeollabuk-do 55365, South Korea
| | - Ara Cho
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju, Jeollabuk-do 55365, South Korea
| | - Yoon Jung Do
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju, Jeollabuk-do 55365, South Korea
| | - Kyoung-Min So
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju, Jeollabuk-do 55365, South Korea
| | - Tai-Young Hur
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju, Jeollabuk-do 55365, South Korea
| | - Sang-Ik Oh
- Laboratory of Veterinary Pathology and Biosafety Research Institute, College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do 54596, South Korea
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2
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Munson E, Carroll KC. Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021. J Clin Microbiol 2023; 61:e0028222. [PMID: 36533910 DOI: 10.1128/jcm.00282-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.
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3
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Isaac S, Flor-Duro A, Carruana G, Puchades-Carrasco L, Quirant A, Lopez-Nogueroles M, Pineda-Lucena A, Garcia-Garcera M, Ubeda C. Microbiome-mediated fructose depletion restricts murine gut colonization by vancomycin-resistant Enterococcus. Nat Commun 2022; 13:7718. [PMID: 36513659 DOI: 10.1038/s41467-022-35380-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
Multidrug-resistant organisms (MDRO) are a major threat to public health. MDRO infections, including those caused by vancomycin-resistant Enterococcus (VRE), frequently begin by colonization of the intestinal tract, a crucial step that is impaired by the intestinal microbiota. However, the specific members of the microbiota that suppress MDRO colonization and the mechanisms of such protection are largely unknown. Here, using metagenomics and mouse models that mimic the patients' exposure to antibiotics, we identified commensal bacteria associated with protection against VRE colonization. We further found a consortium of five strains that was sufficient to restrict VRE gut colonization in antibiotic treated mice. Transcriptomics in combination with targeted metabolomics and in vivo assays indicated that the bacterial consortium inhibits VRE growth through nutrient depletion, specifically by reducing the levels of fructose, a carbohydrate that boosts VRE growth in vivo. Finally, in vivo RNA-seq analysis of each strain of the consortium in combination with ex vivo and in vivo assays demonstrated that a single bacterium (Olsenella sp.) could recapitulate the effect of the consortium. Our results indicate that nutrient depletion by specific commensals can reduce VRE intestinal colonization, which represents a novel non-antibiotic based strategy to prevent infections caused by this multidrug-resistant organism.
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Morinaga K, Kusada H, Sakamoto S, Murakami T, Toyoda A, Mori H, Meng XY, Takashino M, Murotomi K, Tamaki H. Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two strictly anaerobic, Gram-stain-positive, non-motile bacteria (strains OPF53T and TOC12T) were isolated from mouse intestines. Strains OPF53T and TOC12T grew at pH 5.5–9.0 and 5.0–9.0, respectively, and at temperatures of 30–45 °C. The cell morphologies of these strains were short rods and rods, respectively, and the cells possessed intracellular granules. The major cellular fatty acids of OPF53T were C18 : 1
cis 9 and C18 : 1
cis 9 dimethyl acetal, whereas those of TOC12T were C18 : 0 and C18 : 1
cis 9. In OPF53T, the main end-products of modified peptone–yeast extract–glucose (PYG) fermentation were lactate, formate and butyrate, whereas, in addition to these acids, TOC12T also produced hydrogen. The genomes of OPF53T and TOC12T were respectively 2.2 and 2.0 Mbp in size with a DNA G+C contents of 69.1 and 58.7 %. The 16S rRNA gene sequences of OPF53T and TOC12T showed the highest similarity to members of the family
Atopobiaceae
, namely,
Olsenella phocaeensis
Marseille-P2936T (94.3 %) and
Olsenella umbonata
KCTC 15140T (93.2 %), respectively. Phylogenetic analyses revealed that both isolates formed distinct lineages from other genera of the family
Atopobiaceae
. In addition, the two strains were characterized by relatively low 16S rRNA gene sequence similarity (93.4 %) and can be distinguished by their distinctive traits (including cell shape, DNA G+C content, and major fatty acids profiles). On the basis of their polyphasic taxonomic properties, these isolates represent two noel species of two novel genera within the family
Atopobiaceae
, for which the names Granulimonas faecalis gen. nov., sp. nov. (OPF53T=JCM 35015T=KCTC 25474T) and Leptogranulimonas caecicola gen. nov., sp. nov. (TOC12T=JCM 35017T=KCTC 25472T) are proposed.
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Affiliation(s)
- Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hiroyuki Kusada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Sachiko Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Motoko Takashino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Kazutoshi Murotomi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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5
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Lu LF, Yang Y, Zheng L, Zhang R, Liu GQ, Tu TY, Xu T, Luo X, Ran MF, Zhang LQ, Wang ST, Shen CH, Zhang YG. Reclassification of Olsenella gallinarum as Thermophilibacter gallinarum comb. nov. and description of Thermophilibacter immobilis sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu. Int J Syst Evol Microbiol 2021; 71. [PMID: 34914571 DOI: 10.1099/ijsem.0.005192] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, strictly anaerobic, elliptical, non-motile and non-flagellated bacterium, designed LZLJ-2T, was isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu. Growth occurred at 28-45 °C (optimum, 37 °C), at pH 6.0-7.0 (optimum, pH 6.0) and with concentrations of NaCl up to 2 % (w/v; optimum, 0 %). On the basis of 16S rRNA gene sequence similarity, strain LZLJ-2T belonged to the genus Thermophilibacter and was most closely related to Thermophilibacter mediterraneus Marseille-P3256T (similarity 96.9 %), Olsenella gallinarum ClaCZ62T (similarity 96.6 %) and Thermophilibacter provencensis Marseille-P2912T (similarity 96.4 %). In addition, strain LZLJ-2T had high similarity to the genus Olsenella, including Olsenella profusa DSM 13989T (similarity 94.9 %), Olsenella umbonata DSM 22620T (similarity 94.9 %), Olsenella uli ATCC 49627T (similarity 94.22 %), Tractidigestivibacter scatoligenes DSM 28304T (similarity 93.9 %) and Paratractidigestivibacter faecalis KCTC 15699T (similarity 93.25 %). Comparative genome analysis showed that orthoANI values between strain LZLJ-2T and Thermophilibacter mediterraneus Marseille-P3256T, Olsenella gallinarum ClaCZ62T, Thermophilibacter provencensis Marseille-P2912T, Olsenella profusa DSM 13989T, Olsenella umbonata DSM 22620T, Olsenella uli ATCC 49627T, Tractidigestivibacter scatoligenes DSM 28304T and Paratractidigestivibacter faecalis KCTC 15699T were 78.68, 78.99, 78.29, 73.40, 74.00, 74.30, 75.08 and 77.23 %, and the genome-to-genome distance values were respectively 22.3, 22.5, 22.4, 19.6, 20.5, 19.7, 20.5 and 21.5 %. The genomic DNA G+C content of strain LZLJ-2T was 65.21 mol%. The predominant cellular fatty acids (>10 %) of strain LZLJ-2T were C18 : 1 cis 9 (33.7 %), C14 : 0 (22.0 %) and C18 : 1 cis 9 DMA (13.5 %). d-Glucose, sucrose, mannose, maltose, lactose (weak), salicin, glycerol (weak), cellobiose and trehalose (weak) could be used by strain LZLJ-2T as sole carbon sources. Enzyme activity results showed positive reactions with valine arylamidase, leucine arylamidase, crystine arylamidase, acid phosphatase, alkaline phosphatase, esterase (C4) (weakly positive), naphthol-AS-BI-phosphohydrolase, α-glucosidase and β-glucosidase. The major end products of glucose fermentation were lactic acid and acetic acid. It produced skatole from indole acetic acid, and produced p-cresol from modified peptone-yeast extract medium with glucose. Based on the 16S rRNA gene trees as well as the genome core gene tree, it is suggested that Olsenella gallinarum are transferred to genus Thermophilibacter as Thermophilibacter gallinarum comb. nov. Based on phenotypic, genotypic and phylogenetic data, strain LZLJ-2T is considered to represent a novel species of the genus Thermophilibacter, for which the name Thermophilibacter immobilis sp. nov. is proposed. The type strain is LZLJ-2T (=KCTC 25162T=JCM 34224T).
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Affiliation(s)
- Ling-Fei Lu
- Luzhou Laojiao Brewing Co., Ltd., Luzhou 646000, PR China.,Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Yang Yang
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Lei Zheng
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Rui Zhang
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Guang-Qian Liu
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Ting-Yao Tu
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Tao Xu
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Xue Luo
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Mao-Fang Ran
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Li-Qiang Zhang
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Song-Tao Wang
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Cai-Hong Shen
- Luzhou Laojiao Brewing Co., Ltd., Luzhou 646000, PR China.,Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Ying-Gang Zhang
- Luzhou Laojiao Co., Ltd., Luzhou 646000, PR China.,Luzhou Pinchuang Technology Co., Ltd., Luzhou 646000, PR China.,National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
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6
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Zgheib R, Anani H, Meng MM, Mailhe M, Ricaboni D, Morand A, Caputo A, Traore SI, Fontanini A, Armstrong N, Raoult D, Fournier PE. New human-associated species of the family Atopobiaceae and proposal to reclassify members of the genus Olsenella. Int J Syst Evol Microbiol 2021; 71. [PMID: 34047688 DOI: 10.1099/ijsem.0.004819] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Five novel bacterial strains, Marseille-P1476T (=CSURP1476T=DSM 100642T), Marseille-P3256T (=CSURP3256T=CECT 9977T), Marseille-P2936T (=CSURP2936T=DSM 103159T), Marseille-P2912T (=CSURP2912T=DSM 103345T) and Marseille-P3197T (=CSURP3197T=CCUG 71847T), were isolated from various human specimens. These five strains were not identified at the species level by matrix-assisted laser desorption/ionization time of flight mass spectrometry. Following 16S rRNA gene sequence comparisons with the GenBank database, the highest nucleotide sequence similarities of all studied strains were obtained to members of the paraphyletic genus Olsenella. A polyphasic taxono-genomic strategy (16S rRNA gene-based and core genome-based phylogeny, genomic comparison, phenotypic and biochemical characteristics) enabled us to better classify these strains and reclassify Olsenella species. Among the studied strains, Marseille-P1476T, Marseille-P2936T and Marseille-P3197T belonged to new species of the genus Olsenella for which we propose the names Olsenella massiliensis sp. nov., Olsenella phocaeensis sp. nov. and Olsenella urininfantis sp. nov., respectively. Strains Marseille-P2912T and Marseille-P3256T belonged to a new genus for which the names Thermophilibacter provencensis gen. nov., sp. nov. and Thermophilibacter mediterraneus gen. nov., sp. nov. are proposed, respectively. We also propose the creation of the genera Parafannyhessea gen. nov., Tractidigestivibacter gen. nov. and Paratractidigestivibacter gen. nov. and the reclassification of Olsenella umbonata as Parafannyhessea umbonata comb. nov., Olsenella scatoligenes as Tractidigestivibacter scatoligenes comb. nov., and Olsenella faecalis as Paratractidigestivibacter faecalis comb. nov.
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Affiliation(s)
- Rita Zgheib
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Hussein Anani
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Marine Makoa Meng
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Morgane Mailhe
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Davide Ricaboni
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Aurélie Morand
- Pédiatrie spécialisée et médecine infantile, Hôpital de la Timone, AP-HM, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Aurelia Caputo
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sory Ibrahima Traore
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Anthony Fontanini
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Pierre Edouard Fournier
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
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7
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Gryaznova MV, Solodskikh SA, Panevina AV, Syromyatnikov MY, Dvoretskaya YD, Sviridova TN, Popov ES, Popov VN. Study of microbiome changes in patients with ulcerative colitis in the Central European part of Russia. Heliyon 2021; 7:e06432. [PMID: 33748490 PMCID: PMC7970149 DOI: 10.1016/j.heliyon.2021.e06432] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 01/05/2021] [Accepted: 03/03/2021] [Indexed: 12/31/2022] Open
Abstract
Ulcerative colitis (UC) is an inflammatory disease that affects the colon and rectum. Recently, evidence has emerged about the influence of microbiota on the development of this disease. However, studies on the role of intestinal microbiota in the pathogenesis of UC have been incomplete. In addition, there are no comprehensive studies of the causes of ulcerative colitis and data on the microbiological composition of the intestines of patients with ulcerative colitis in Russia. We carried out a study of the microbiological composition of the intestines of patients with ulcerative colitis and healthy individuals. We found significant changes in the bacteria genera and species in patients with UC compared with the control group using sequencing on the IonTorrent PGM system and subsequent data analysis. In our study we observed a significant increase of the genus Haemophilus, Olsenella, Prevotella, Cedecea, Peptostreptococcus, Faecalibacterium, Lachnospira, Negativibacillus, Butyrivibrio, and the species Bacteroides coprocola, Phascolarctobacterium succinatutens, Dialister succinatiphilus, Sutterella wadsworthensis, Faecalibacterium prausnitzii in patients with ulcerative colitis. In addition, in patients with ulcerative colitis there was a significant decrease in the genus Fusicatenibacter, Butyricimonas, Lactococcus, Eisenbergiella, Coprobacter, Cutibacterium, Falsochrobactrum, Brevundimonas, Yersinia, Leuconostoc and in the species Fusicatenibacter saccharivorans. We found confirmation of our data with literary sources and studies of UC. In addition, we discovered a few taxa such as Negativibacillus spp. and Falsochrobactrum spp. that have not been previously found in human stool samples. Our data confirm that more research is needed to understand the role of microbiome changes in the development of UC in different people populations.
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Affiliation(s)
- M V Gryaznova
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia.,Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - S A Solodskikh
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia.,Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - A V Panevina
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - M Y Syromyatnikov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia.,Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Yu D Dvoretskaya
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia.,Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - T N Sviridova
- Department of Hospital Therapy and Endocrinology, Voronezh State Medical University Named After N.N. Burdenko, 394036 Voronezh, Russia.,Family Medicine Center "Olympus of Health", 394036 Voronezh, Russia
| | - E S Popov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - V N Popov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia.,Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
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Abudabos AM, Abdelrahman MM, Alatiyat RM, Aljumaah MR, Al Jassim R, Stanley D. Effect of dietary inclusion of graded levels of distillers dried grains with solubles on the performance, blood profile and rumen microbiota of Najdi lambs. Heliyon 2021; 7:e05683. [PMID: 33553711 PMCID: PMC7848638 DOI: 10.1016/j.heliyon.2020.e05683] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/02/2020] [Accepted: 12/04/2020] [Indexed: 12/26/2022] Open
Abstract
An experiment was conducted in a completely randomized design to evaluate the effect of including graded levels (0, 20, 30, 40 and 50% of diet) of dried distiller's grains with solubles (DDGS) on growth performance, slaughter parameters, blood serum metabolites and rumen microbiota in weaned Najdi male lambs. Thirty-five lambs, initial body weight of 33.45 ± 0.75 kg, and approximately three-month old were used in a 94-day feeding experiment. Performance measurements were conducted biweekly and blood samples were collected monthly. Inclusion of DDGS in the diets of growing Najdi lambs at levels up to 50% did not affect body weight gain (BWG) compared with the lambs fed the control diet (CON, 0% DDGS). Lambs fed the 50% DDGS diet consumed less feed compared with lambs in other groups (98 vs 112.5 kg DM) but had no adverse effect on BWG. Rumen pH values at 0, 6, 12 and 18 h post feeding and concentrations of blood serum total proteins, glucose, triglycerides, urea-N or albumin were similar across treatments. Slaughter parameters including slaughter weight, hot and cold carcass weights and dressing % (hot and cold carcass) were not affected by the treatments. There was no difference in the weights of full compartmental stomach and intestines, liver, omental fat, Kidney Knob and Channel Fat (KKCF) and tail fat between DDGS treatments and CON. The study concluded that the inclusion of DDGS in the diets of growing Najdi lambs had no adverse effects on growth performance and slaughter parameters. Rumen microbiota was not affected, however, our data suggest significant interactions between DDGS and selected bacterial groups and DDGS driven rearrangement of Prevotella species.
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Affiliation(s)
- A M Abudabos
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - M M Abdelrahman
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - R M Alatiyat
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - M R Aljumaah
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - R Al Jassim
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia 4072, Australia
| | - D Stanley
- Central Queensland University, Institute for Future Farming Systems, Rockhampton QLD 4702, Australia
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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