1
|
Li Y, Zhang D, Bo D, Peng D, Sun M, Zheng J. A taxonomic note on the order Caryophanales: description of 12 novel families and emended description of 21 families. Int J Syst Evol Microbiol 2024; 74. [PMID: 39556488 DOI: 10.1099/ijsem.0.006539] [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] [Indexed: 11/20/2024] Open
Abstract
The order Caryophanales, belonging to class Bacilli, is globally distributed in various ecosystems. Currently, this order comprised 12 families that show vast phenotypic, ecological and genotypic variation. The classification of Caryophanales at the family level is currently mainly based on 16S rRNA gene sequencing analysis and the presence of shared phenotypic characteristics, resulting in noticeable anomalies. Our present study revises the taxonomy of Caryophanales based on 1080 available high-quality genome sequences of type strains. The evaluated parameters included the core-genome phylogeny, pairwise average aa identity, lineage-specific core genes, physiological criteria and ecological parameters. Based on the results of this polyphasic approach, we propose that the order Caryophanales be reclassified into 41 families, which include the existing 12 families, 17 families in a recent Validation List in the IJSEM (Validation List no. 215) and 12 novel families for which we propose the names Aureibacillaceae, Cytobacillaceae, Domibacillaceae, Falsibacillaceae, Heyndrickxiaceae, Lottiidibacillaceae, Oxalophagaceae, Pradoshiaceae, Rossellomoreaceae, Schinkiaceae, Sulfoacidibacillaceae and Sutcliffiellaceae. This work represents a genomic sequence-based and systematic framework for classifying the order Caryophanales at the family level, providing new insights into its evolution.
Collapse
Affiliation(s)
- Yangjie Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Dechao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dexin Bo
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Donghai Peng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Ming Sun
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jinshui Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, PR China
| |
Collapse
|
2
|
Munson E, Burbick CR, Lawhon SD, Krueger T, Ruiz-Reyes E. Valid and accepted novel bacterial taxa isolated from non-domestic animals and taxonomic revisions published in 2023. J Clin Microbiol 2024; 62:e0104224. [PMID: 39352133 PMCID: PMC11481486 DOI: 10.1128/jcm.01042-24] [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] [Indexed: 10/17/2024] Open
Abstract
Continued investigation into the bacteria associated with non-domestic animals provides important information for recognizing normal flora, assessing the health status of these unique species of animals, and identifying new or emerging pathogens of concern. In this summary of novel taxa and taxonomic revisions, considerable additions have been made toward understanding fecal and mucosal flora in multiple wild animal species. In addition, novel pathogenic bacteria are discussed, including multiple Chlamydia spp. causing disease in a hawk and crocodile, two Corynebacterium spp. causing oral lesions in penguins and a lesser-known genus, Mergibacter within Family Pasteurellaceae, causing disease in multiple wild bird species. Finally, a few revisions to bacteria isolated from normal non-domestic animal body sites are mentioned.
Collapse
Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Trinity Krueger
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elena Ruiz-Reyes
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| |
Collapse
|
3
|
Lawhon SD, Burbick CR, Munson E, Zapp A, Thelen E, Villaflor M. Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142522. [PMID: 36533958 PMCID: PMC9945507 DOI: 10.1128/jcm.01425-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.
Collapse
Affiliation(s)
- Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Maia Villaflor
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| |
Collapse
|
4
|
Ribeiro IDA, Bach E, Passaglia LMP. Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family. Mol Phylogenet Evol 2022; 177:107624. [PMID: 36084857 DOI: 10.1016/j.ympev.2022.107624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/26/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022]
Abstract
Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.
Collapse
Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Evelise Bach
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil.
| |
Collapse
|
5
|
Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:2355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
Collapse
Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
| | | |
Collapse
|
6
|
Ndongo S, Beye M, Labas N, Di Pinto F, Richez M, Lagier JC, Fournier PE, Raoult D, Bittar F. Gorillibacterium timonense sp. nov., isolated from an obese patient. Arch Microbiol 2020; 202:1223-1229. [PMID: 32103285 DOI: 10.1007/s00203-020-01834-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/28/2019] [Accepted: 02/11/2020] [Indexed: 01/15/2023]
Abstract
A Gram-negative and facultative anaerobic bacterium, designated strain SN4T, was isolated from the stool sample of an obese Amazonian patient. The new isolate was characterized by the taxonogenomics approach. The strain SN4T was beige-colored, circular and not haemolytic. Cells are rod shaped and motile with several flagella. Strain SN4T grows optimally at pH 7 and can survive in the presence of a saline concentration of up to 75 g/l NaCl. The 16S ribosomal RNA gene sequence analysis of the novel strain SN4T showed 95.28% similarity in nucleotide sequence with Gorillibacterium massiliense G5T, the phylogenetically closest neighbor and the type species of this genus. Anteiso-C15:0, iso-C15:0 and C16:0 were found as the major components in the cellular fatty acid analysis of this isolate. The genomic draft of strain SN4T is 5,263,742 bp long with 53.33% of G+C content. The differences in physiological, biochemical characteristics and phylogenetic and genomic data make it possible to clearly distinguish the strain SN4T from G. massiliense G5T. Based on the taxonogenomic description and the phenotypic and biochemical characteristics of this bacterium presented in this article, we propose the SN4T strain (= CSUR P2011 = DSM 100,698) as a new species, Gorillibacterium timonense sp. nov.
Collapse
Affiliation(s)
- Sokhna Ndongo
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Mamadou Beye
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Noémie Labas
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Fabrizio Di Pinto
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Magali Richez
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Jean-Christophe Lagier
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Fadi Bittar
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France.
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
| |
Collapse
|
7
|
Chen RW, Zhang J, He YQ, Wang KX, Li C, Long LJ. Longirhabdus pacifica gen. nov., sp. nov., isolated from a deep-sea hydrothermal sediment in the West Pacific Ocean. Int J Syst Evol Microbiol 2019; 69:3362-3367. [PMID: 31622228 DOI: 10.1099/ijsem.0.003526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative bacterium, designated as SCSIO 06110T, was isolated from a deep-sea sediment of the West Pacific Ocean. Cells were 0.5-0.8 µm in width and 3.0-4.0 µm in length, spore-forming, rod-shaped with peritrichous flagella. Positive for catalase and urease, negative for oxidase and nitrate reduction. Growth occurred at 15-37 °C, pH 6-9 and 1-5 % (w/v) NaCl, with optimum growth at 28 °C, pH 7 and 3 % (w/v) NaCl. MK-7 was the only menaquinone. The strain possessed diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids. Iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0 were the major fatty acids. The novel isolate clustered with genera in the family Paenibacillaceae, but formed a separated branch with the closest relative Chengkuizengella sediminis J15A17T (91.1 % sequence similarity) when compared in a phylogenetic analysis of 16S rRNA gene sequences. The DNA G+C content of strain SCSIO 06110T was 38.5 mol%. Based on the polyphasic data presented, a new genus, Longirhabdus gen. nov., is proposed in the family Paenibacillaceae with the type species Longirhabdus pacifica sp. nov. and the type strain SCSIO 06110T (=DSM 105158T=CGMCC 1.16550T).
Collapse
Affiliation(s)
- Rou-Wen Chen
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Jing Zhang
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Yuan-Qiu He
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Ke-Xin Wang
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Cun Li
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Li-Juan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| |
Collapse
|
8
|
Davoust B, Levasseur A, Mediannikov O. Studies of nonhuman primates: key sources of data on zoonoses and microbiota. New Microbes New Infect 2018; 26:S104-S108. [PMID: 30402252 PMCID: PMC6205567 DOI: 10.1016/j.nmni.2018.08.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 12/11/2022] Open
Abstract
The genetic and morphologic similarities between primates and humans means that much information obtained from primates may be applied to humans, and vice versa. However, habitat loss, hunting and the continued presence of humans have a negative effect on the biology and behaviour of almost all nonhuman primates. Noninvasive methods such as stool collection are among the safest alternative ways to study the multiple aspects of the biology of primates. Many epidemiologic issues (e.g. pathogen detection, microbiota studies) may be easily studied using stool samples from primates. Primates are undoubtedly among the first candidates suspected of becoming the source of one of the next emerging epidemic of zoonotic origin, as has already been observed with HIV, malaria and monkeypox. The Institut Hospitalo-Universitaire Méditerranée Infection in Marseille actively participates in the study, mostly epidemiologic, of nonhuman primates, using mostly stool samples.
Collapse
Affiliation(s)
- B Davoust
- Microbes, Evolution, Phylogeny and Infection (MEФI), UMR Aix-Marseille Université, IRD, APHM, IHU Méditerranée Infection, Marseille, France
| | - A Levasseur
- Microbes, Evolution, Phylogeny and Infection (MEФI), UMR Aix-Marseille Université, IRD, APHM, IHU Méditerranée Infection, Marseille, France
| | - O Mediannikov
- Microbes, Evolution, Phylogeny and Infection (MEФI), UMR Aix-Marseille Université, IRD, APHM, IHU Méditerranée Infection, Marseille, France
| |
Collapse
|
9
|
Hwang WM, Ko Y, Kang K, Ahn TY. Paludirhabdus telluriireducens gen. nov., sp. nov. and Paludirhabdus pumila sp. nov., isolated from soil of a mountain wetland and emended description of Gorillibacterium massiliense. Int J Syst Evol Microbiol 2018; 68:3040-3046. [PMID: 30067175 DOI: 10.1099/ijsem.0.002946] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of Gram-stain-positive, endospore-forming, motile by means of peritrichous flagella, aerobic or facultative anaerobic, and rod-shaped bacteria that were designated ON8T and ON6T were isolated from soil collected from a mountain wetland in Gwang-ju, Republic of Korea. The isolates were catalase-positive and oxidase-negative. Cells of ON8T and ON6T grew at 15-35 °C (optimal 30 °C) and 15-40 °C (optimal 30 °C), respectively. The major menaquinone was MK-7 and the major cellular fatty acids (>10 % of the total) were anteiso-C15 : 0, iso-C15 : 0, C14 : 0 and C16 : 0. The predominant polar lipids were diphosphatidylglycerol, aminophospholipid and phospholipid. Meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C contents of strains ON8T and ON6T were 50.6 and 53.5 mol%, respectively, and the 16S rRNA gene sequence analysis showed that the nearest phylogenetic neighbour of both strains was Gorillibacterium massiliense G5T (93.9 %), followed by the members of the genus Paenibacillus in the family Paenibacillaceae. The DNA-DNA hybridization relatedness value between ON8T and ON6T was 44.1 %, which indicated that they represented distinct species. Based on polyphasic characteristics, a novel genus is proposed with the name Paludirhabdus gen. nov., which consists of two species, Paludirhabdus telluriireducens sp. nov. (the type species; type strain ON8T=KACC 19267T=JCM 31958T) and Paludirhabdus pumila sp. nov. (type strain ON6T=KACC 19266T=JCM 31957T).
Collapse
Affiliation(s)
- Woon Mo Hwang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Yongseok Ko
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Tae-Young Ahn
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| |
Collapse
|
10
|
Ndongo S, Lagier JC, Raoult D, Fournier PE. Gorillibacterium timonense sp. nov. and Vitreoscilla massiliensis sp. nov., two new bacterial species isolated from stool specimens of obese Amazonian patients. New Microbes New Infect 2018; 23:48-51. [PMID: 29556410 PMCID: PMC5854890 DOI: 10.1016/j.nmni.2018.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/09/2018] [Indexed: 12/22/2022] Open
Abstract
We report the main characteristics of Gorillibacterium timonense strain SN4T sp. nov. and Vitreoscilla massiliensis strain SN6T sp. nov., two new bacterial species isolated from stool specimens of obese Amazonian patients.
Collapse
Affiliation(s)
- S. Ndongo
- UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée-Infection, Marseille, France
| | - J.-C. Lagier
- UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée-Infection, Marseille, France
| | - D. Raoult
- UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée-Infection, Marseille, France
| | - P.-E. Fournier
- UMR VITROME, Aix-Marseille Université, IRD, SSA, AP-HM, IHU Méditerranée-Infection, Marseille, France
| |
Collapse
|
11
|
Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:529-531. [DOI: 10.1099/ijsem.0.001845] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| |
Collapse
|
12
|
Hadjadj L, Tidjani Alou M, Sokhna C, Lagier JC, Raoult D, Rolain JM. Genome sequence and description of Desnuesiella massiliensis gen. nov., sp. nov. a new member of family Clostridiaceae. New Microbes New Infect 2016; 11:84-90. [PMID: 27158511 PMCID: PMC4845082 DOI: 10.1016/j.nmni.2016.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/12/2016] [Accepted: 03/14/2016] [Indexed: 11/03/2022] Open
Abstract
Desnuesiella massiliensis, strain MT10(T) gen. nov., sp. nov. is a newly proposed genus within the family Clostridiaceae, isolated from the digestive microbiota of a child suffering from kwashiorkor. Desnuesiella massiliensis is a facultatively anaerobic, Gram-positive rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5 503 196-bp long genome (one chromosome but no plasmid) contains 5227 protein-coding and 81 RNA genes, including 14 rRNA genes.
Collapse
Affiliation(s)
- L. Hadjadj
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - M. Tidjani Alou
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - C. Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - J.-C. Lagier
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - D. Raoult
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.-M. Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| |
Collapse
|
13
|
Bittar F, Keita MB, Lagier JC, Peeters M, Delaporte E, Raoult D. Gorilla gorilla gorilla gut: a potential reservoir of pathogenic bacteria as revealed using culturomics and molecular tools. Sci Rep 2014; 4:7174. [PMID: 25417711 PMCID: PMC4241516 DOI: 10.1038/srep07174] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/31/2014] [Indexed: 11/13/2022] Open
Abstract
Wild apes are considered to be the most serious reservoir and source of zoonoses. However, little data are available about the gut microbiota and pathogenic bacteria in gorillas. For this propose, a total of 48 fecal samples obtained from 21 Gorilla gorilla gorilla individuals (as revealed via microsatellite analysis) were screened for human bacterial pathogens using culturomics and molecular techniques. By applying culturomics to one index gorilla and using specific media supplemented by plants, we tested 12,800 colonies and identified 147 different bacterial species, including 5 new species. Many opportunistic pathogens were isolated, including 8 frequently associated with human diseases; Mycobacterium bolletii, Proteus mirabilis, Acinetobacter baumannii, Klebsiella pneumoniae, Serratia marcescens, Escherichia coli, Staphylococcus aureus and Clostridium botulinum. The genus Treponema accounted for 27.4% of the total reads identified at the genus level via 454 pyrosequencing. Using specific real-time PCR on 48 gorilla fecal samples, in addition to classical human pathogens, we also observed the fastidious bacteria Bartonella spp. Borrelia spp., Coxiella burnetii and Tropheryma whipplei in the gorilla population. We estimated that the prevalence of these pathogens vary between 4.76% and 85.7%. Therefore, gorillas share many bacterial pathogens with humans suggesting that they could be a reservoir for their emergence.
Collapse
Affiliation(s)
- Fadi Bittar
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - Mamadou B Keita
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - Martine Peeters
- Institut de Recherche pour le Développement, University Montpellier 1, UMI 233, Montpellier, France
| | - Eric Delaporte
- Institut de Recherche pour le Développement, University Montpellier 1, UMI 233, Montpellier, France
| | - Didier Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| |
Collapse
|