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Oren A, Göker M. Validation List no. 219. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2024; 74:006452. [PMID: 39360699 PMCID: PMC11447935 DOI: 10.1099/ijsem.0.006452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Indexed: 10/04/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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He JH, Wang CY, Abdugheni R, Ni X, Liu C, Bi MX, Liu SJ. Acutalibacter caecimuris sp. nov., Acutalibacter intestini sp. nov. and Neglectibacter caecimuris sp. nov. , three novel species of the family Oscillospiraceae isolated from caecal contents of C57BL/6J mice. Int J Syst Evol Microbiol 2024; 74:006449. [PMID: 38995185 PMCID: PMC11316587 DOI: 10.1099/ijsem.0.006449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
The intestines of mice are colonized by diverse, as-yet-uncultivated bacteria. In this report, we describe the isolation, culture, genotypic and phenotypic characterization, as well as taxonomic classification of three novel anaerobic bacterial strains derived from the caecal contents of C57BL/6J male mice. According to the phenotypic and genotype-based polyphasic taxonomy, we propose three novel species within the family Oscillospiraceae. They are Acutalibacter caecimuris sp. nov. (type strain M00118T=CGMCC 1.18042T=KCTC 25739T), Acutalibacter intestini sp. nov. (type strain M00204T=CGMCC 1.18044T=KCTC 25741T) and Neglectibacter caecimuris sp. nov. (type strain M00184T=CGMCC 1.18043T=KCTC 25740T).
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Affiliation(s)
- Jia-Hui He
- College of Veterinary Medicine, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Jinzhong 030801, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chang-Yu Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, PR China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Xue Ni
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Ming-Xia Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
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Okuma K, Hatayama K, Tokuno H, Ebara A, Odachi A, Masuyama H, Hoshiko N, Tanaka N. A risk estimation method for depression based on the dysbiosis of intestinal microbiota in Japanese patients. Front Psychiatry 2024; 15:1382175. [PMID: 38863614 PMCID: PMC11165696 DOI: 10.3389/fpsyt.2024.1382175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Introduction Early detection of depression is important for preventing depression-related suicides and reducing the risk of recurrence. This study explored the association between depression and intestinal microbiota and developed a depression risk-estimation method based on this. Methods The intestinal microbiota of Japanese patients with depression (33 males and 35 females) and disease-free controls (246 males and 384 females) in their 20's to 60's were compared by sex using 16S rRNA gene amplicon sequencing. A depression-risk estimation method was developed using structural equation modeling. Results Intestinal bacteria taxa that differed between depression and control groups were identified based on effect size (absolute value greater than 0.2). Neglecta was more abundant, while Coprobacter, Butyricimonas, Clostridium_XlVb, and Romboutsia were less abundant in the male depression group compared to the male control group. In the female depression group, Massilimicrobiota, Merdimonas, and Sellimonas were more abundant, whereas Dorea and Agathobacter were less abundant compared to the female control group. Several of the intestinal bacterial taxa that were less abundant in depression were associated with butyrate or hydrogen production. Using these depression-associated intestinal bacteria as indicators, risk-estimation models using structural equation modeling for depression were developed. In the risk-estimation models for males and females, the areas under the receiver operating characteristic curve were 0.72 and 0.70, respectively, indicating that these models can distinguish between individuals with and without depression. Conclusions This study provides insights into depression etiology and aids in its early detection and treatment.
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Affiliation(s)
| | | | - Hidetaka Tokuno
- Symbiosis Solutions Inc., Tokyo, Japan
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Aya Ebara
- Symbiosis Solutions Inc., Tokyo, Japan
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Abou Chacra L, Bonnet M, Heredia M, Haddad G, Armstrong N, Alibar S, Bretelle F, Fenollar F. Peptoniphilus genitalis sp. nov. and Mobiluncus massiliensis sp. nov.: Novel Bacteria Isolated from the Vaginal Microbiome. Curr Microbiol 2024; 81:97. [PMID: 38372813 PMCID: PMC10876752 DOI: 10.1007/s00284-023-03584-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/07/2023] [Indexed: 02/20/2024]
Abstract
The strains Marseille-Q7072T (= CSUR Q7072T = CECT 30604 T) and Marseille-Q7826T (= CSUR Q7826T = CECT 30727 T) were isolated from vaginal samples. As MALDI-TOF mass spectrometry failed to identify them, their genomes were directly sequenced to determine their taxogenomic identities. Both strains are anaerobic without any oxidase and catalase activity. C16:0 is the most abundant fatty acid for both strains. Strain Marseille-Q7072T is non-spore-forming, non-motile, Gram-stain-positive, and coccus-shaped, while strain Marseille-Q7826T is non-spore-forming, motile, Gram-stain-variable, and curved rod-shaped. The genomic comparison of the Marseille-Q7072T and Marseille-Q7826T strains showed that all digital DNA-DNA hybridisation (dDDH) and mean orthologous nucleotide identity (OrthoANI) values were below published species thresholds (70% and 95-96%, respectively) with other closely related species with standing in nomenclature. Thus, we conclude that both strains are new bacterial species. Strain Marseille-Q7072T is a new member of the Bacillota phylum, for which the name Peptoniphilus genitalis sp. nov. is proposed, while the Marseille-Q7826T strain is a new member of the Actinomycetota phylum, for which the name Mobiluncus massiliensis sp. nov. is proposed.
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Affiliation(s)
- Linda Abou Chacra
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Marion Bonnet
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Mégane Heredia
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Gabriel Haddad
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | | | | | - Florence Bretelle
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- Department of Gynaecology and Obstetrics, Gynépole, La Conception, AP-HM, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée Infection, Marseille, France.
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Abou Chacra L, Benatmane A, Iwaza R, Ly C, Alibar S, Armstrong N, Mediannikov O, Bretelle F, Fenollar F. Culturomics reveals a hidden world of vaginal microbiota with the isolation of 206 bacteria from a single vaginal sample. Arch Microbiol 2023; 206:20. [PMID: 38095693 PMCID: PMC10721685 DOI: 10.1007/s00203-023-03742-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/05/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023]
Abstract
The composition of the vaginal microbiota is known to be influenced by various factors and to be associated with several disorders affecting women's health. Although metagenomics is currently a widely used method for studying the human microbiota, it has certain limitations, such as a lack of information on bacterial viability. It is therefore important to use culture-based methods such as culturomics. Here, we used 35 different culture conditions to comprehensively characterize the vaginal bacterial diversity of a single woman's flora. A total of 206 bacterial species, belonging to six phyla (for a little more than half to Firmicutes, followed mainly by Actinobacteria, Bacteroidetes, and Proteobacteria) and 45 families, and 2 fungal species were cultivated. While several species of lactobacilli have been isolated, a wide variety of other bacteria were also separated, including 65 never reported before in vaginal flora, including a new bacterial species, Porphyromonas vaginalis sp. nov. Extensive culture-based methods are essential to establish a comprehensive, evidence-based repertoire of bacterial viability. If combined with molecular methods, they can provide a much more thorough understanding of the vaginal microbiota and fulfil the unknown part of metagenomic studies.
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Affiliation(s)
- Linda Abou Chacra
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Amel Benatmane
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Rim Iwaza
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Claudia Ly
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | | | | | - Oleg Mediannikov
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Florence Bretelle
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Department of Gynecology and Obstetrics, AP-HM, Gynépole, La Conception, Marseille, France
| | - Florence Fenollar
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.
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Abou Chacra L, Bonnet M, Heredia M, Haddad G, Armstrong N, Alibar S, Bretelle F, Fenollar F. Cellulomonas endometrii sp. nov.: a novel bacterium isolated from the endometrial microbiota. Arch Microbiol 2023; 205:377. [PMID: 37940730 PMCID: PMC10632280 DOI: 10.1007/s00203-023-03703-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023]
Abstract
An isolate of a bacterium recovered from an endometrial biopsy failed to be identified by MALDI-TOF mass spectrometry and was subjected to 16S rRNA sequencing. The obtained sequence was compared by BLASTn against the NCBI database, which revealed that the most closely related species was Cellulomonas hominis and Cellulomonas pakistanensis, with 98.85% and 98.45% identity, respectively. Phenotypic characterisation and genome sequencing were performed. The isolate was facultative anaerobic, gram-positive, motile, non-spore forming, and rod-shaped. Cell wall fatty acid profiling revealed that 12-methyl-tetradecanoic acid was the most abundant fatty acid (36%). The genome size was 4.25 Mbp with a G + C content of 74.8 mol%. Genomic comparison of species closely related to this strain showed that all digital DNA-DNA hybridisation (dDDH) and mean orthologous nucleotide identity (OrthoANI) values were below published species thresholds (70% and 95-96%, respectively). Based on these data, we conclude that this isolate represents a new bacterial species belonging to the family Cellulomonadaceae and the phylum Actinomycetota. We propose the name Cellulomonas endometrii sp. nov. The type strain is Marseille-Q7820T (= CSUR Q7820 = CECT 30716).
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Affiliation(s)
- Linda Abou Chacra
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Marion Bonnet
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Mégane Heredia
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | | | | | | | - Florence Bretelle
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- Department of Gynaecology and Obstetrics, Gynépole, La Conception, AP-HM, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée Infection, Marseille, France.
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Liu J, Robinson K, Lyu W, Yang Q, Wang J, Christensen KD, Zhang G. Anaerobutyricum and Subdoligranulum Are Differentially Enriched in Broilers with Disparate Weight Gains. Animals (Basel) 2023; 13:1834. [PMID: 37889711 PMCID: PMC10251939 DOI: 10.3390/ani13111834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 10/29/2023] Open
Abstract
The intestinal microbiota is critically important for animal health and productivity. However, the influence of the intestinal microbiota on animal growth efficiency remains elusive. This current study was aimed at identifying the intestinal bacteria that are associated with the growth rate of broilers in a commercial production setting. Ross 708 broilers with extremely high, medium, and extremely low body weight (BW) were separately selected for each sex from a house of approximately 18,000 chickens on day 42. The cecal content of each animal was subjected to 16S rRNA gene sequencing for microbiota profiling. Our results indicate that a number of bacteria were differentially enriched among different groups of broilers, with several showing a significant correlation (p < 0.05) with BW in both sexes or in a sex-specific manner. Subdoligranulum was drastically diminished in high-BW birds with a strong negative correlation with BW in both males and females. While one Anaerobutyricum strain showed a positive correlation with BW in both sexes, another strain of Anaerobutyricum was positively correlated with BW only in females. These sex-dependent and -independent bacteria could be targeted for improving the growth efficiency and may also be explored as potential biomarkers for the growth rate of broiler chickens.
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Affiliation(s)
- Jing Liu
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA; (J.L.); (K.R.); (W.L.); (Q.Y.); (J.W.)
| | - Kelsy Robinson
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA; (J.L.); (K.R.); (W.L.); (Q.Y.); (J.W.)
- Poultry Research Unit, USDA–Agricultural Research Service, Starkville, MS 39759, USA
| | - Wentao Lyu
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA; (J.L.); (K.R.); (W.L.); (Q.Y.); (J.W.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qing Yang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA; (J.L.); (K.R.); (W.L.); (Q.Y.); (J.W.)
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jing Wang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA; (J.L.); (K.R.); (W.L.); (Q.Y.); (J.W.)
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | | | - Guolong Zhang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA; (J.L.); (K.R.); (W.L.); (Q.Y.); (J.W.)
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Anaerococcus ihuae sp. nov. and Mediannikoviicoccus vaginalis gen. nov., sp. nov., two new bacteria isolated from human vaginal samples. Arch Microbiol 2022; 204:508. [PMID: 35859139 PMCID: PMC9300522 DOI: 10.1007/s00203-022-03082-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/11/2022]
Abstract
Strains Marseille-Q5893 (= CSUR Q5893 = CECT 30496) and Marseille-Q5883 (= CSUR Q5883 = CECT 30497) were isolated from vaginal samples using the culturomics approach. The 16S rRNA gene sequences of each strain were sequenced and then compared by BLASTn to the NCBI database. Strains Marseille-Q5893 and Marseille-Q5883 were most closely related to Anaerococcus obesiensis and Finegoldia magna, with identities of 98.5% and 90.0%, respectively. Strain Marseille-Q5893 is strictly anaerobic, while strain Marseille-Q5883 is facultative anaerobic. Both strains are Gram-positive, coccus-shaped, oxidase- and catalase-negative. The most abundant fatty acid for both strains is hexadecanoic acid, followed by 9-octadecenoic acid and tetradecanoic acid. Strain Marseille-Q5893 has a genome size of 1,831,271 bp with a G+C content of 29.4 mol%, whereas strain Marseille-Q5883 has a genome of 1,997,945 bp with a 33.6 mol% G+C content. The genomic comparison of closely related species with strains Marseille-Q5893 and Marseille-Q5883 showed that all digital DNA–DNA hybridization (dDDH) and orthologous average nucleotide identity (OrthoANI) values were lower than the published species thresholds (70% and 95–96%, respectively). Based on these data, we conclude that strain Marseille-Q5893 belongs to a new species in the family Peptoniphilaceae and strain Marseille-Q5883 belongs to a new genus in the family Peptostreptococcaceae. For these two new bacterial species, the names Anaerococcus ihuae sp. nov. and Mediannikoviicoccus vaginalis gen. nov., sp. nov., were proposed.
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Iwaza R, Abou Chacra L, Ibrahim A, Pham TPT, Lo CI, Tidjani Alou M, Sokhna C, Raoult D, Lagier JC. Description of Ornithinibacillus massiliensis sp. nov., Isolated from a Child with Marasmus. Curr Microbiol 2022; 79:262. [PMID: 35852643 DOI: 10.1007/s00284-022-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022]
Abstract
A Gram-positive, aerobic, motile, endospore-forming, rod-shaped bacterium was isolated from a stool sample of a child with marasmus. The 16S rRNA gene showed that strain Marseille-P3601T exhibited 98.68% sequence identity with Ornithinibacillus scapharcae strain TW25. The genomic DNA G+C contents of this strain was 36.9 mol%. The fatty acid profiles of the strain were iso/anteiso branched structures. The highest DDH value was 20.6%, shared with O. californiensis, amongst its closest strain phylogenetically. Based on the phylogenetic position and the genomic, morphological, and biochemical properties, strain Marseille-P3601T (=CSUR P3601=CCUG 71291) represents a novel species in the genus Ornithinibacillus, for which the name Ornithinibacillus massiliensis sp. nov. is proposed.
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Affiliation(s)
- Rim Iwaza
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Linda Abou Chacra
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Ahmad Ibrahim
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Thi Phuong Thao Pham
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Maryam Tidjani Alou
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Cheikh Sokhna
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Campus Communication, UCAD-IRD of Hann, Dakar, Senegal
| | - Didier Raoult
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Jean-Christophe Lagier
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France. .,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
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