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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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2
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Neugent ML, Hulyalkar NV, Kumar A, Xing C, Zimmern PE, Shulaev V, De Nisco NJ. Urinary Glycosaminoglycans Are Associated with Recurrent UTI and Urobiome Ecology in Postmenopausal Women. ACS Infect Dis 2023; 9:1022-1032. [PMID: 36942838 PMCID: PMC10111421 DOI: 10.1021/acsinfecdis.3c00027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Glycosaminoglycans (GAGs) are linear, negatively charged polysaccharides composed of repeating disaccharide units of uronic acid and amino sugars. The luminal surface of the bladder epithelium is coated with a GAG layer. These urothelial GAGs are thought to provide a protective barrier and serve as a potential interaction site with the urinary microbiome (urobiome). Previous studies have profiled urinary GAG composition in mixed cohorts, but the urinary GAG composition in postmenopausal women remains undefined. To investigate the relationship between GAGs and recurrent urinary tract infection (rUTI), we profiled urinary GAGs in a controlled cohort of postmenopausal women. We found that chondroitin sulfate (CS) is the major urinary GAG in postmenopausal women and that urinary CS was elevated in women with active rUTI. We also associated urinary GAGs with urobiome composition and identified bacterial species that significantly associated with urinary GAG concentration. Corynebacterium amycolatum, Porphyromonas somerae, and Staphylococcus pasteuri were positively associated with heparin sulfate or hyaluronic acid, and bacterial species associated with vaginal dysbiosis were negatively correlated with urinary CS. Altogether, this work defines changes in urinary GAG composition associated with rUTI and identifies new associations between urinary GAGs and the urobiome that may play a role in rUTI pathobiology.
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Affiliation(s)
- Michael L Neugent
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Neha V Hulyalkar
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Philippe E Zimmern
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Vladimir Shulaev
- Department of Biological Sciences, The University of North Texas, Denton, Texas 76203, United States
- Advanced Environmental Research Institute, The University of North Texas, Denton, Texas 76203, United States
| | - Nicole J De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
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3
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Neugent ML, Hulyalkar NV, Kumar A, Xing C, Zimmern PE, Shulaev V, De Nisco NJ. Urinary Glycosaminoglycans are Associated with Recurrent UTI and Urobiome Ecology in Postmenopausal Women. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523678. [PMID: 36711817 PMCID: PMC9882061 DOI: 10.1101/2023.01.11.523678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Glycosaminoglycans (GAGs) are linear, negatively charged polysaccharides composed of repeating disaccharide units of uronic acid and amino sugars. The luminal surface of the bladder epithelium is coated with a GAG layer. These urothelial GAGs are thought to provide a protective barrier and serve as a potential interaction site with the urinary microbiome (urobiome). Previous studies have profiled urinary GAG composition in mixed cohorts, but the urinary GAG composition in postmenopausal women remains undefined. To investigate the relationship between GAGs and recurrent UTI (rUTI), we profiled urinary GAGs in a controlled cohort of postmenopausal women. We found that chondroitin sulfate (CS) is the major urinary GAG in postmenopausal women and that urinary CS was elevated in women with active rUTI. We also associated urinary GAGs with urobiome composition and identified bacterial species that significantly associated with urinary GAG concentration. Corynebacterium amycolatum, Porphyromonas somerae , and Staphylococcus pasteuri were positively associated with heparin sulfate or hyaluronic acid and bacterial species associated with vaginal dysbiosis were negatively correlated to urinary CS. Altogether, this work defines changes in urinary GAG composition associated with rUTI and identifies new associations between urinary GAGs and the urobiome that may play a role in rUTI pathobiology.
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4
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Neugent ML, Kumar A, Hulyalkar NV, Lutz KC, Nguyen VH, Fuentes JL, Zhang C, Nguyen A, Sharon BM, Kuprasertkul A, Arute AP, Ebrahimzadeh T, Natesan N, Xing C, Shulaev V, Li Q, Zimmern PE, Palmer KL, De Nisco NJ. Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome. Cell Rep Med 2022; 3:100753. [PMID: 36182683 PMCID: PMC9588997 DOI: 10.1016/j.xcrm.2022.100753] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/28/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022]
Abstract
Postmenopausal women are severely affected by recurrent urinary tract infection (rUTI). The urogenital microbiome is a key component of the urinary environment. However, changes in the urogenital microbiome underlying rUTI susceptibility are unknown. Here, we perform shotgun metagenomics and advanced culture on urine from a controlled cohort of postmenopausal women to identify urogenital microbiome compositional and function changes linked to rUTI susceptibility. We identify candidate taxonomic biomarkers of rUTI susceptibility in postmenopausal women and an enrichment of lactobacilli in postmenopausal women taking estrogen hormone therapy. We find robust correlations between Bifidobacterium and Lactobacillus and urinary estrogens in women without urinary tract infection (UTI) history. Functional analyses reveal distinct metabolic and antimicrobial resistance gene (ARG) signatures associated with rUTI. Importantly, we find that ARGs are enriched in the urogenital microbiomes of women with rUTI history independent of current UTI status. Our data suggest that rUTI and estrogen shape the urogenital microbiome in postmenopausal women.
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Affiliation(s)
- Michael L Neugent
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Neha V Hulyalkar
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Kevin C Lutz
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Vivian H Nguyen
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Jorge L Fuentes
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cong Zhang
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Amber Nguyen
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Belle M Sharon
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Amy Kuprasertkul
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amanda P Arute
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Tahmineh Ebrahimzadeh
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Nitya Natesan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, The University of North Texas, Denton, TX, USA; Advanced Environmental Research Institute, The University of North Texas, Denton, TX, USA
| | - Qiwei Li
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Philippe E Zimmern
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Nicole J De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA; Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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5
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Mbaye B, Lo CI, Dione N, Benabdelkader S, Tidjani Alou M, Brahimi S, Armstrong N, Alibar S, Raoult D, Moal V, Million M, Fournier PE, Fenollar F. Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., isolated from humans. Arch Microbiol 2022; 204:506. [PMID: 35857142 PMCID: PMC9300514 DOI: 10.1007/s00203-022-03044-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022]
Abstract
Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive coccoid bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37 °C in anaerobic conditions. They also metabolize carbohydrates, such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains. The highest digital DNA–DNA hybridization (dDDH) values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. Strains Marseille-P3761 and Marseille-P3195 shared an OrthoANI value of 83.5% which was the highest value found with Peptoniphilus species studied here. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that Peptoniphilus coli sp. nov., and Peptoniphilus urinae sp. nov., are new species for which strains Marseille-P3761 (CSUR P3761 = CCUG 71,569) and Marseille-P3195 (CSUR P3195 = DSM 103,468) are their type strains, respectively of two new Peptoniphilus species, for which we propose the names Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., respectively.
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Affiliation(s)
- Babacar Mbaye
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Niokhor Dione
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Sarah Benabdelkader
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Maryam Tidjani Alou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Samy Brahimi
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Nicholas Armstrong
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Stéphane Alibar
- IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Valérie Moal
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,AP-HM, Hôpital Conception, Centre de Néphrologie Et Transplantation Rénale, Centre Hospitalo-Universitaire Conception, Marseille, France
| | - Matthieu Million
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France. .,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
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6
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Wang H, Yang JL, Chen C, Zheng Y, Chen M, Qi J, Tang S, Zhan XY. Identification of Peptoniphilus vaginalis-Like Bacteria, Peptoniphilus septimus sp. nov., From Blood Cultures in a Cervical Cancer Patient Receiving Chemotherapy: Case and Implications. Front Cell Infect Microbiol 2022; 12:954355. [PMID: 35880078 PMCID: PMC9307962 DOI: 10.3389/fcimb.2022.954355] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
A 39-year-old woman with a 3-year human papillomavirus (HPV) 18 infection history was admitted to the hospital for a 16-day history of vaginal bleeding after sex. She was diagnosed with cervical cancer based on the results of the electronic colposcopy, cervical cytology, microscopy, and magnetic resonance imaging (MRI). Then, she received chemotherapy, with paclitaxel 200 mg (day 1), cisplatin 75 mg (day 2), and bevacizumab 700 mg (day 3) twice with an interval of 27 days. During the examination for the diagnosis and treatment, many invasive operations, including removal of intrauterine device, colposcopy, and ureteral dilatation, were done. After that, the patient was discharged and entered the emergency department about 2.5 months later with a loss of consciousness probably caused by septic shock. The patient finally died of multiple organ failure and bacterial infection, although she has received antimicrobial therapy. The blood cultures showed a monobacterial infection with an anaerobic Gram-positive bacterial strain, designated as SAHP1. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI–TOF MS) indicated that the patient was infected with Peptoniphilus asaccharolyticus, while molecular analysis and genome-based taxonomy confirmed the infection with a novel Peptoniphilus species that has a close genetic relationship with Peptoniphilus vaginalis and proposed provisionally as Peptoniphilus septimus sp. nov., which may also act as a commensal of the human vagina. Genomic features of SAHP1 have been fully described, and comparative genomic analysis reveals the known prokaryote relative of Peptoniphilus septimus sp. nov. in the genus Peptoniphilus. The invasive operations on the genital tract during the diagnosis and treatment of the patient and the tumor tissue damage and bleeding may have a certain role in the bloodstream infection. This study casts a new light on the Peptoniphilus bacteria and prompts clinicians to include anaerobic blood cultures as part of their blood culture procedures, especially on patients with genital tract tumors. Furthermore, due to the incomplete database and unsatisfying resolution of the MALDI–TOF MS for Peptoniphilus species identification, molecular identification, especially whole-genome sequencing, is required for those initially identified as bacteria belonging to Peptoniphilus in the clinical laboratory.
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Affiliation(s)
- Huacheng Wang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jin-Lei Yang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Chunmei Chen
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Ying Zheng
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- School of Clinical Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Mingming Chen
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Junhua Qi
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shihuan Tang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xiao-Yong Zhan
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- *Correspondence: Xiao-Yong Zhan,
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7
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Huang C, Callahan BJ, Wu MC, Holloway ST, Brochu H, Lu W, Peng X, Tzeng JY. Phylogeny-guided microbiome OTU-specific association test (POST). MICROBIOME 2022; 10:86. [PMID: 35668471 PMCID: PMC9171974 DOI: 10.1186/s40168-022-01266-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The relationship between host conditions and microbiome profiles, typically characterized by operational taxonomic units (OTUs), contains important information about the microbial role in human health. Traditional association testing frameworks are challenged by the high dimensionality and sparsity of typical microbiome profiles. Phylogenetic information is often incorporated to address these challenges with the assumption that evolutionarily similar taxa tend to behave similarly. However, this assumption may not always be valid due to the complex effects of microbes, and phylogenetic information should be incorporated in a data-supervised fashion. RESULTS In this work, we propose a local collapsing test called phylogeny-guided microbiome OTU-specific association test (POST). In POST, whether or not to borrow information and how much information to borrow from the neighboring OTUs in the phylogenetic tree are supervised by phylogenetic distance and the outcome-OTU association. POST is constructed under the kernel machine framework to accommodate complex OTU effects and extends kernel machine microbiome tests from community level to OTU level. Using simulation studies, we show that when the phylogenetic tree is informative, POST has better performance than existing OTU-level association tests. When the phylogenetic tree is not informative, POST achieves similar performance as existing methods. Finally, in real data applications on bacterial vaginosis and on preterm birth, we find that POST can identify similar or more outcome-associated OTUs that are of biological relevance compared to existing methods. CONCLUSIONS Using POST, we show that adaptively leveraging the phylogenetic information can enhance the selection performance of associated microbiome features by improving the overall true-positive and false-positive detection. We developed a user friendly R package POSTm which is freely available on CRAN ( https://CRAN.R-project.org/package=POSTm ). Video Abstract.
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Affiliation(s)
- Caizhi Huang
- Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA
| | - Benjamin J Callahan
- Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, 27607, USA
| | - Michael C Wu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, 98109, USA
| | - Shannon T Holloway
- Department of Statistics, North Carolina State University, Raleigh, 27606, USA
| | - Hayden Brochu
- Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, 27607, USA
| | - Wenbin Lu
- Department of Statistics, North Carolina State University, Raleigh, 27606, USA
| | - Xinxia Peng
- Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, 27607, USA
| | - Jung-Ying Tzeng
- Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA.
- Department of Statistics, North Carolina State University, Raleigh, 27606, USA.
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8
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Barberis C, Litterio M, Venuta ME, Maldonado ML, Abel S, Fernández-Canigia L, Vaustat D, Azula N, Castello L, Legaria MC, Pereyra A, Rossetti A, Predari SC, Rollet R, Cejas D. The dilemma of identifying Peptoniphilus species by using two MALDI-TOF MS systems. Anaerobe 2021; 73:102500. [PMID: 34890813 DOI: 10.1016/j.anaerobe.2021.102500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 11/16/2021] [Accepted: 12/05/2021] [Indexed: 12/31/2022]
Abstract
Two commercial MALDI-TOF MS systems were used to identify 18 isolates, belonging to the Peptoniphilus genus; also the 16S rRNA sequencing identity was compared against the MALDI-TOF MS system results. Bruker Biotyper system provided higher accuracy than Vitek MS system, however, adding spectra could allow a more reliable species level identification.
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Affiliation(s)
- Claudia Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina.
| | | | | | | | - Sofía Abel
- Hospital de Pediatría Garrahan, Buenos Aires, Argentina
| | | | - Daniela Vaustat
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Natalia Azula
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno (CEMIC), Buenos Aires, Argentina
| | - Liliana Castello
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Cristina Legaria
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina
| | - Ana Pereyra
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Microbiología, Buenos Aires, Argentina
| | - Adelaida Rossetti
- Hospital Interzonal de Agudos Presidente Perón de Avellaneda, Provincia de Buenos Aires, Argentina
| | - Silvia Carla Predari
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - Raquel Rollet
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Daniela Cejas
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Buenos Aires, Argentina
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9
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Ben Khedher M, Diouf FS, Lo CI, Alibar S, Durand G, Raoult D, Fournier PE, Fenollar F. Collinsella ihumii sp. nov., a new anaerobic bacterium isolated from human stool. Arch Microbiol 2021; 203:6315-6322. [DOI: 10.1007/s00203-021-02562-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
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10
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Aujoulat F, Mazuet C, Criscuolo A, Popoff MR, Enault C, Diancourt L, Jumas-Bilak E, Lavigne JP, Marchandin H. Peptoniphilus nemausensis sp. nov. A new Gram-positive anaerobic coccus isolated from human clinical samples, an emendated description of the genus Peptoniphilus and an evaluation of the taxonomic status of Peptoniphilus species with not validly published names. Syst Appl Microbiol 2021; 44:126235. [PMID: 34385044 DOI: 10.1016/j.syapm.2021.126235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/27/2022]
Abstract
A Gram-positive, anaerobic coccus isolated from a human surgical site infection was previously shown to belong to an unknown species of the genus Peptoniphilus initially proposed as 'Peptoniphilus nemausus' sp. nov., based on both 16S rRNA gene sequence identity of 97.9% with the most closely related species Peptoniphilus coxii and an individualized phylogenetic branching within the genus Peptoniphilus. A polyphasic characterization of the novel species is proposed herein. Whole genome sequence analysis showed an average nucleotide identity value of 84.75% and digital DNA-DNA hybridization value of 28.9% against P. coxii type strain. The strain displayed unique features among members of the genus Peptoniphilus, as it was able to hydrolyze aesculin, and produced acetate as the major metabolic end-product without associated production of butyrate. Growth was observed under microaerophilic conditions. From all these data, the isolate is confirmed as belonging to a new Peptoniphilus species, for which the name Peptoniphilus nemausensis sp. nov. is proposed. The type strain is 1804121828T (=LMG 31466T = CECT 9935T). A database survey using a highly polymorphic partial sequence of the 16S rRNA gene of P. nemausensis revealed P. nemausensis to be a particularly rare skin-associated species in humans. An emendated description of the Peptoniphilus genus is proposed based on a review of the characteristics of the 12 new species with validly published names since the genus description in 2001 and of P. nemausensis. Finally, the relationships between members of the genus Peptoniphilus were explored based on whole genome sequence analysis in order to clarify the taxonomic status of not yet validly published species showing that three pairs of species should be considered as synonyms: Peptoniphilus timonensis and 'Peptoniphilus phoceensis', Peptoniphilus lacydonensis and 'Peptoniphilus rhinitidis', Peptoniphilus tyrrelliae and Peptoniphilus senegalensis.
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Affiliation(s)
- Fabien Aujoulat
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Christelle Mazuet
- Centre National de Référence bactéries anaérobies et botulisme, Institut Pasteur, Paris, France
| | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Michel R Popoff
- Unité des Toxines Bactériennes, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Cécilia Enault
- Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Laure Diancourt
- Centre National de Référence bactéries anaérobies et botulisme, Institut Pasteur, Paris, France
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Département d'Hygiène Hospitalière, CHU Montpellier, Montpellier, France
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Univ Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France.
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11
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Mbaye B, Tidjani Alou M, Fadlane A, Fregiere L, Alibar S, Million M, Fenollar F, Lo CI. Neobacillus massiliamazoniensis sp. nov., a new bacterial species isolated from stool sample of an inhabitant of the Amazon region. New Microbes New Infect 2021; 42:100900. [PMID: 34168882 PMCID: PMC8209264 DOI: 10.1016/j.nmni.2021.100900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/16/2021] [Accepted: 05/09/2021] [Indexed: 11/26/2022] Open
Abstract
Using a culturomics approach, a strain was isolated, identified and characterised following the taxonogenomics concept. Neobacillus massiliamazoniensis sp. nov., strain LF1T (=CSURP1359) was isolated from human stool. The 16S rRNA gene sequence analysis of strain LF1T (accession number: LK021124) exhibits 98.32% similarity levels with Neobacillus bataviensis strain IDA1115 (accession number: NR_036766.1), the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain LF1T (accession number: CVRB00000000) is 4.6 Mbp with a G+C content of 34.1 mol%. Analysis of phylogenic tree, genomic analysis and phenotypic criteria described here sufficiently prove that this bacterium is different from previously known bacterial species with standing in nomenclature and represents a new Neobacillus species belonging to Firmicutes phylum.
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Affiliation(s)
- B Mbaye
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Tidjani Alou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - A Fadlane
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - L Fregiere
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - S Alibar
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Million
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - F Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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12
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Wei ZT, Chen HL, Wang CF, Yang GL, Han SM, Zhang SL. Depiction of Vaginal Microbiota in Women With High-Risk Human Papillomavirus Infection. Front Public Health 2021; 8:587298. [PMID: 33490017 PMCID: PMC7820762 DOI: 10.3389/fpubh.2020.587298] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/08/2020] [Indexed: 01/14/2023] Open
Abstract
Persistent infection with the carcinogenic human papillomavirus (HPV) is a prerequisite for the progression of cervical lesions and cancer. A growing body of research has focused on the functional role of the vaginal microbiota in the persistence of HPV infection. Understanding the microbial composition and structure in women with high-risk (hr)-HPV infection may help reveal associations between the vaginal microbiota and HPV infection, and identify potential biomarkers. Our study investigated the vaginal microbial community in women with and without hr-HPV infection, by using 16s rRNA gene sequencing. We found that microbial perturbations occurred in the early phase of hr-HPV infection. Lactobacillus and Sporolactobacillus were decreased, while bacteria related to bacterial vaginosis (BV), such as Gardnerella, Prevotella, Dialister, Slackia, Actinomyces, Porphyromonas, Peptoniphilus, Anaerococcus, Peptostreptococcus, Streptococcus, Ureaplasma, Megasphaera, and Mycoplasma were increased. Our results could offer insights into the correlations between hr-HPV and the vaginal microbiota in the early infection period, and provide indications that the predominance of some BV-associated bacteria during hr-HPV infection may increase the risk for cervical neoplasia.
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Affiliation(s)
- Zhen-Tong Wei
- Department of Oncologic Gynecology, The First Hospital of Jilin University, Changchun, China
| | - Hong-Liang Chen
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
| | - Chun-Feng Wang
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
| | - Gui-Lian Yang
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
| | - Shu-Mei Han
- Medical Department, The First Hospital of Jilin University, Changchun, China
| | - Song-Ling Zhang
- Department of Oncologic Gynecology, The First Hospital of Jilin University, Changchun, China
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13
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Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome. mSphere 2020; 5:5/6/e00448-20. [PMID: 33208514 PMCID: PMC7677004 DOI: 10.1128/msphere.00448-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment but also to the use of conflicting methodologies to study its microbial composition. Here, we systematically assessed best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region performed best in silico, but limitations of current sequencing technologies meant that the V3-V4 region performed equally well. Both approaches presented very good agreement with qPCR quantification of key taxa, provided that an appropriate bioinformatic pipeline was used. Shotgun metagenomic sequencing presents an interesting alternative to 16S rRNA gene amplification and sequencing but requires deeper sequencing and more bioinformatic expertise and infrastructure. We assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and -use reference database of vaginal taxa. This curated database performed as well as the best-performing previously published strategies. Despite the many advantages of shotgun sequencing, none of the shotgun approaches assessed here agreed with the qPCR data as well as the 16S rRNA gene sequencing.IMPORTANCE The vaginal microbiome has been connected to various aspects of host health, including susceptibility to sexually transmitted infections as well as gynecological cancers and pregnancy outcomes. This has led to a thriving research environment but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.
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14
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Bordigoni A, Lo C, Yimagou EK, Nicaise B, Diop K, Raoult D, Desnues C, Fenollar F. Two new bacteria isolated from vagina of a patient with vaginosis: Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov. New Microbes New Infect 2020; 38:100771. [PMID: 33204431 PMCID: PMC7652708 DOI: 10.1016/j.nmni.2020.100771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/09/2020] [Accepted: 09/27/2020] [Indexed: 12/21/2022] Open
Abstract
Two new bacterial strains, Marseille-P4126 (=CSURP4126) and Marseille-P4593 (=CSURP4593), were isolated from the vaginal sample of a French woman with vaginosis. These strains were identified and characterized using the taxonogenomics method. The findings from phylogenetic tree interpretation, phenotypic criteria and genomic analysis provided here distinctly display that Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov. are new members of the genus Atopobium and Butyricimonas, respectively.
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Affiliation(s)
- A. Bordigoni
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - E. Kuete Yimagou
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - B. Nicaise
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - K. Diop
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C. Desnues
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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15
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Elwood C, Albert A, McClymont E, Wagner E, Mahal D, Devakandan K, Quiqley BL, Pakzad Z, Yudin MH, Hill JE, Money D. Different and diverse anaerobic microbiota were seen in women living with HIV with unsuppressed HIV viral load and in women with recurrent bacterial vaginosis: a cohort study. BJOG 2019; 127:250-259. [PMID: 31498547 DOI: 10.1111/1471-0528.15930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To compare the vaginal microbiota of women living with HIV (WLWH) with the vaginal microbiota of women with recurrent bacterial vaginosis (BV) and healthy women without HIV to determine if there are differences in the vaginal microbiome, what factors influence these differences, and to characterise HIV clinical parameters including viral load and CD4 count in relation to the vaginal microbiome. DESIGN Observational cohort study. SETTING Canada. POPULATION Women aged 18-49 years who were premenopausal and not pregnant were recruited into three cohorts: healthy women, WLWH and women with recurrent BV. METHODS Demographic and clinical data were collected via interviews and medical chart reviews. Vaginal swabs were collected for Gram-stain assessment and microbiome profiling using the cpn60 barcode sequence. MAIN OUTCOME MEASURES To compare overall community composition differences, we used compositional data analysis methods, hierarchical clustering and Kruskal-Wallis tests where appropriate. RESULTS Clinical markers such as odour and abnormal discharge, but not irritation, were associated with higher microbial diversity. WLWH with unsuppressed HIV viral loads were more likely than other groups to have non-Gardnerella-dominated microbiomes. HIV was associated with higher vaginal microbial diversity and this was related to HIV viral load, with unsuppressed women demonstrating significantly higher relative abundance of Megasphaera genomosp. 1, Atopobium vaginae and Clostridiales sp. (all P < 0.05) compared with all other groups. CONCLUSIONS In WLWH, unsuppressed HIV viral loads were associated with a distinct dysbiotic profile consisting of very low levels of Lactobacillus and high levels of anaerobes. TWEETABLE ABSTRACT Vaginal microbiomes in WLWH with viral load >50 copies/ml have distinct dysbiotic profiles with high levels of anaerobes.
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Affiliation(s)
- C Elwood
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Women's Health Research Institute, Vancouver, BC, Canada
| | - Ayk Albert
- Women's Health Research Institute, Vancouver, BC, Canada
| | - E McClymont
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Women's Health Research Institute, Vancouver, BC, Canada
| | - E Wagner
- Women's Health Research Institute, Vancouver, BC, Canada
| | - D Mahal
- Women's Health Research Institute, Vancouver, BC, Canada
| | - K Devakandan
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Women's Health Research Institute, Vancouver, BC, Canada
| | - B L Quiqley
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Z Pakzad
- Women's Health Research Institute, Vancouver, BC, Canada
| | - M H Yudin
- Department of Obstetrics and Gynaecology, St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - J E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - D Money
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Women's Health Research Institute, Vancouver, BC, Canada
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16
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Enault C, Aujoulat F, Pantel A, Cellier N, Lechiche C, Mégy B, Lavigne JP, Marchandin H. Surgical site infection after hip replacement due to a novel Peptoniphilus species, provisionally named 'Peptoniphilus nemausus' sp. nov. Anaerobe 2019; 61:102071. [PMID: 31306754 DOI: 10.1016/j.anaerobe.2019.102071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/06/2019] [Accepted: 07/11/2019] [Indexed: 12/23/2022]
Abstract
We report a case of surgical site infection after total hip prosthesis replacement due to an ofloxacin-resistant Peptoniphilus isolate belonging to an unknown species for which the name 'Peptoniphilus nemausus' sp. nov. is proposed. Follow-up was favourable under clindamycin and rifampin for 3 months in this patient whom had a Proteus mirabilis infection treated by fluoroquinolone.
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Affiliation(s)
- Cécilia Enault
- Department of Microbiology, Nîmes University Hospital, Nîmes, France
| | - Fabien Aujoulat
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | - Alix Pantel
- National Institute of Health and Medical Research, INSERM U1047, University of Montpellier, Department of Microbiology, CHU Nîmes, Nîmes, France
| | - Nicolas Cellier
- Department of Orthopaedic Surgery, Nîmes University Hospital, Nîmes, France
| | - Catherine Lechiche
- Department of Infectious Diseases, Nîmes University Hospital, Nîmes, France
| | - Bernard Mégy
- Department of Orthopaedic Surgery, Nîmes University Hospital, Nîmes, France
| | - Jean-Philippe Lavigne
- National Institute of Health and Medical Research, INSERM U1047, University of Montpellier, Department of Microbiology, CHU Nîmes, Nîmes, France
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Department of Microbiology, CHU Nîmes, Nîmes, France.
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17
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Togo A, Diop A, Camara A, Kuete E, Konate S, Brevaut V, Des Robert C, Delerce J, Armstrong N, Roussel Y, Fournier PE, Thera M, Raoult D, Million M. Lactimicrobium massiliense gen. nov., sp. nov.; Anaerolactibacter massiliensis gen. nov., sp. nov.; Galactobacillus timonensis gen. nov., sp. nov. and Acidipropionibacterium timonense sp. nov. isolated from breast milk from healthy breastfeeding African women. New Microbes New Infect 2019; 29:100537. [PMID: 31011429 PMCID: PMC6462784 DOI: 10.1016/j.nmni.2019.100537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 01/10/2023] Open
Abstract
Four strains isolated by microbial culturomics from breast milk of healthy mothers from Mali were not identified and characterized by taxono-genomics. This led us to propose the new genera and species Lactimicrobium massiliense, Anaerolactibacter massiliensis and Galactobacillus timonensis containing type strain Marseille-P4301T (CSUR P4301T), Marseille-P4302T (CSUR P4302T) and Marseille-P4641T (CSUR P4641T), respectively. The strain Marseille-P4482 represents a novel species, Acidipropionibacterium timonense, in a previously known genus with type strain being Marseille-P4482T (CSUR P4482T).
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Affiliation(s)
- A.H. Togo
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - A. Diop
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - A. Camara
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - E. Kuete
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - S. Konate
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - V. Brevaut
- APHM, CHU Hôpital Nord, Service de médecine néonatale, Marseille, France
| | - C. Des Robert
- APHM, CHU Hôpital de la Conception, Service de médecine néonatale, F-13385, Marseille, France
| | - J. Delerce
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - N. Armstrong
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Y. Roussel
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M.A. Thera
- Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, FMOS-FAPH, University of Science, Techniques and Technologies, Bamako, Mali
| | - D. Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M. Million
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
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18
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Diop K, Diop A, Michelle C, Richez M, Rathored J, Bretelle F, Fournier PE, Fenollar F. Description of three new Peptoniphilus species cultured in the vaginal fluid of a woman diagnosed with bacterial vaginosis: Peptoniphilus pacaensis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilus vaginalis sp. nov. Microbiologyopen 2018; 8:e00661. [PMID: 29931836 PMCID: PMC6436483 DOI: 10.1002/mbo3.661] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/05/2018] [Accepted: 04/30/2018] [Indexed: 12/19/2022] Open
Abstract
Three previously unidentified Gram‐positive anaerobic coccoid bacteria, strains KhD‐2T, KHD4T, and Kh‐D5T, isolated from a vaginal swab, were characterized using the taxonogenomics concept. The phylogenic analysis, phenotypic characteristics, and genotypic data presented in this report attest that these three bacteria are distinct from previously known bacterial species with standing in nomenclature and represent three new Peptoniphilus species. Strain KhD‐2T is most closely related to Peptoniphilus sp. DNF00840 and Peptoniphilus harei (99.7% and 98.2% identity, respectively); strain KHD4T to Peptoniphilus lacrimalis (96%) and strain Kh‐D5T to Peptoniphilus coxii (97.2%). Strains KhD‐2T, KHD4T, and Kh‐D5TDNA G+C contents are, respectively, 34.23%, 31.87%, and 49.38%; their major fatty acid was C16:0 (41.6%, 32.0%, and 36.4%, respectively). We propose that strains KhD‐2T (=CSUR P0125 = DSM 101742), KHD4T (=CSUR P0110 = CECT 9308), and Kh‐D5T (=CSUR P2271 = DSM 101839) be the type strains of the new species for which the names Peptoniphilus vaginalis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilu pacaensis sp. nov., are proposed, respectively.
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Affiliation(s)
- Khoudia Diop
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Awa Diop
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Caroline Michelle
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Magali Richez
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Jaishriram Rathored
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Florence Bretelle
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Department of Gynecology and Obstetrics, Gynépole, Hôpital Nord, AP-HM, Marseille, France
| | | | - Florence Fenollar
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
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