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George SD, Van Gerwen OT, Dong C, Sousa LGV, Cerca N, Elnaggar JH, Taylor CM, Muzny CA. The Role of Prevotella Species in Female Genital Tract Infections. Pathogens 2024; 13:364. [PMID: 38787215 PMCID: PMC11123741 DOI: 10.3390/pathogens13050364] [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: 04/04/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Female genital tract infections (FGTIs) include vaginal infections (e.g., bacterial vaginosis [BV]), endometritis, pelvic inflammatory disease [PID], and chorioamnionitis [amniotic fluid infection]. They commonly occur in women of reproductive age and are strongly associated with multiple adverse health outcomes including increased risk of HIV/sexually transmitted infection acquisition and transmission, infertility, and adverse birth outcomes such as preterm birth. These FGTIs are characterized by a disruption of the cervicovaginal microbiota which largely affects host immunity through the loss of protective, lactic acid-producing Lactobacillus spp. and the overgrowth of facultative and strict anaerobic bacteria. Prevotella species (spp.), anaerobic Gram-negative rods, are implicated in the pathogenesis of multiple bacterial FGTIs. Specifically, P. bivia, P. amnii, and P. timonensis have unique virulence factors in this setting, including resistance to antibiotics commonly used in treatment. Additionally, evidence suggests that the presence of Prevotella spp. in untreated BV cases can lead to infections of the upper female genital tract by ascension into the uterus. This narrative review aims to explore the most common Prevotella spp. in FGTIs, highlight their important role in the pathogenesis of FGTIs, and propose future research in this area.
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Affiliation(s)
- Sheridan D. George
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (O.T.V.G.); (C.D.); (C.A.M.)
| | - Olivia T. Van Gerwen
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (O.T.V.G.); (C.D.); (C.A.M.)
| | - Chaoling Dong
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (O.T.V.G.); (C.D.); (C.A.M.)
| | - Lúcia G. V. Sousa
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal; (L.G.V.S.); (N.C.)
| | - Nuno Cerca
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal; (L.G.V.S.); (N.C.)
| | - Jacob H. Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (J.H.E.); (C.M.T.)
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (J.H.E.); (C.M.T.)
| | - Christina A. Muzny
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (O.T.V.G.); (C.D.); (C.A.M.)
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A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter. Syst Appl Microbiol 2022; 45:126354. [DOI: 10.1016/j.syapm.2022.126354] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 11/19/2022]
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Young W, Maclean P, Dunstan K, Ryan L, Peters J, Armstrong K, Anderson R, Dewhurst H, van Gendt M, Dilger RN, Dekker J, Haggarty N, Roy N. Lacticaseibacillus rhamnosus HN001 alters the microbiota composition in the cecum but not the feces in a piglet model. Front Nutr 2022; 9:1002369. [PMID: 36386940 PMCID: PMC9650270 DOI: 10.3389/fnut.2022.1002369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/28/2022] [Indexed: 12/03/2022] Open
Abstract
The probiotic Lacticaseibacillus rhamnosus strain HN001 has been shown to have several beneficial health effects for both pediatric and maternal groups, including reduced risk of eczema in infants and gestational diabetes and postnatal depression in mothers. While L. rhamnosus HN001 appears to modify immune and gut barrier biomarkers, its mode of action remains to be fully elucidated. To gain insights into the role of HN001 on the infant microbiome, the impacts of L. rhamnosus HN001 supplementation was studied in 10-day old male piglets that were fed either infant formula, or infant formula with L. rhamnosus HN001 at a low (1.3 × 105 CFU/ml) or high dose (7.9 × 106 CFU/ml) daily for 24 days. The cecal and fecal microbial communities were assessed by shotgun metagenome sequencing and host gene expression in the cecum and colon tissue was assessed by RNA-seq. Piglet fecal samples showed only modest differences between controls and those receiving dietary L. rhamnosus HN001. However, striking differences between the three groups were observed for cecal samples. While total lactobacilli were significantly increased only in the high dose L. rhamnosus HN001 group, both high and low dose groups showed an up to twofold reduction across the Firmicutes phylum and up to fourfold increase in Prevotella compared to controls. Methanobrevibacter was also decreased in HN001 fed piglets. Microbial genes involved in carbohydrate and vitamin metabolism were among those that differed in relative abundance between those with and without L. rhamnosus HN001. Changes in the cecal microbiome were accompanied by increased expression of tight junction pathway genes and decreased autophagy pathway genes in the cecal tissue of piglets fed the higher dose of L. rhamnosus HN001. Our findings showed supplementation with L. rhamnosus HN001 caused substantial changes in the cecal microbiome with likely consequences for key microbial metabolic pathways. Host gene expression changes in the cecum support previous research showing L. rhamnosus HN001 beneficially impacts intestinal barrier function. We show that fecal samples may not adequately reflect microbiome composition higher in the gastrointestinal tract, with the implication that effects of probiotic consumption may be missed by examining only the fecal microbiome.
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Affiliation(s)
- Wayne Young
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
- *Correspondence: Wayne Young,
| | - Paul Maclean
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Kelly Dunstan
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Leigh Ryan
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Jason Peters
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Kelly Armstrong
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Rachel Anderson
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Hilary Dewhurst
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | | | - Ryan N. Dilger
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - James Dekker
- Fonterra Research and Development Centre, Palmerston North, New Zealand
| | - Neill Haggarty
- Fonterra Research and Development Centre, Palmerston North, New Zealand
| | - Nicole Roy
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
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Identification of trypsin-degrading commensals in the large intestine. Nature 2022; 609:582-589. [PMID: 36071157 PMCID: PMC9477747 DOI: 10.1038/s41586-022-05181-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 08/02/2022] [Indexed: 11/23/2022]
Abstract
Increased levels of proteases, such as trypsin, in the distal intestine have been implicated in intestinal pathological conditions1–3. However, the players and mechanisms that underlie protease regulation in the intestinal lumen have remained unclear. Here we show that Paraprevotella strains isolated from the faecal microbiome of healthy human donors are potent trypsin-degrading commensals. Mechanistically, Paraprevotella recruit trypsin to the bacterial surface through type IX secretion system-dependent polysaccharide-anchoring proteins to promote trypsin autolysis. Paraprevotella colonization protects IgA from trypsin degradation and enhances the effectiveness of oral vaccines against Citrobacter rodentium. Moreover, Paraprevotella colonization inhibits lethal infection with murine hepatitis virus-2, a mouse coronavirus that is dependent on trypsin and trypsin-like proteases for entry into host cells4,5. Consistently, carriage of putative genes involved in trypsin degradation in the gut microbiome was associated with reduced severity of diarrhoea in patients with SARS-CoV-2 infection. Thus, trypsin-degrading commensal colonization may contribute to the maintenance of intestinal homeostasis and protection from pathogen infection. Colonization of trypsin-degrading commensal bacteria may contribute to the maintenance of intestinal homeostasis and protection against pathogen infection in humans and mice.
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Yao H, Lu S, Williams BA, Flanagan BM, Gidley MJ, Mikkelsen D. Absolute abundance values reveal microbial shifts and co-occurrence patterns during gut microbiota fermentation of dietary fibres in vitro. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Ueki A, Tonouchi A, Kaku N, Ueki K. Prevotella herbatica sp. nov., a plant polysaccharide-decomposing anaerobic bacterium isolated from a methanogenic reactor. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005221] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately anaerobic bacterial strain (WR041T) was isolated from a plant residue sample in a methanogenic reactor. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming rods.
Prevotella paludivivens
JCM 13650T was the closest species of the strain based on 16S rRNA gene sequencing (98.9 % similarity). Genome analysis of strain WR041T indicated that the genome size of the strain was 3.52 Mb and the genomic DNA G+C content was 37.5 mol%. Although the 16S rRNA gene sequence similarity of strain WR041T with the closest species was higher than the threshold value of the recommended species delineation (98.7 %), the average nucleotide identity and the digital DNA–DNA hybridization value between them were 91–92 and 45.5 %, respectively, suggesting that strain WR041T represents a novel species in the genus. Strain WR041T essentially required haemin and CO2/Na2CO3 for growth. The strain was saccharolytic and decomposed various polysaccharides (glucomannan, inulin, laminarin, pectin, starch and xylan) and produced acetate and succinate. The optimum growth conditions were 35 °C and pH 6.8. The major cellular fatty acids were branched-chain fatty acids such as anteiso-C15 : 0 and iso-C15 : 0. Menaquinones MK-11 and MK-12 were the major respiratory quinones. Many protein-coding genes which were not found in the genome of
P. paludivivens
as orthologous genes were detected in the genome of strain WR041T. Based on the differences in the phylogenetic, genomic and physiological characteristics between strain WR041T and related species, the name Prevotella herbatica sp. nov. is proposed to accommodate strain WR041T (=NBRC 115134T = DSM 112534T).
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Affiliation(s)
- Atsuko Ueki
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Nobuo Kaku
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
| | - Katsuji Ueki
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
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Buhl MEJ, Meier-Kolthoff JP, Marschal M. Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid. Int J Syst Evol Microbiol 2021; 71. [PMID: 34908520 DOI: 10.1099/ijsem.0.005146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately anaerobic strain, designated as A2931T, was isolated from oropharyngeal abscess puncture fluid of a patient sampled during routine care at a hospital and further characterized both phenotypically, biochemically and genotypically. This Gram-negative rod-shaped bacterium was moderately saccharolytic and proteolytic. Phylogenetic analyses of full-length 16S rRNA gene and whole-genome sequences revealed it to be best placed in the genus Prevotella, but to be only comparatively distantly related to recognized species, with the closest relationship to Prevotella baroniae (average nucleotide identity and digital DNA-DNA hybridization values both well below the generally accepted thresholds). Strain A2931T had a genomic DNA G+C content of 47.7 mol%. Its most abundant cellular long-chain fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. Taken together, this polyphasic data suggests strain A2931T to represent a novel species within the genus Prevotella, for which the name Prevotella illustrans sp. nov. is proposed. The type strain is A2931T (=DSM 108028T=CCOS 1232T=CCUG 72806T). Interestingly, we found strain A2931T to correspond to the oral taxon Prevotella HMT-820 in the Human Oral Microbiome Database, as supported by overall genome relatedness index analyses >99 %. Thus, our work not only closes one of the gaps of knowledge about hitherto unnamed species isolated from humans, but also will facilitate identification of this taxon both in the clinical microbiology context and in research alike.
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Affiliation(s)
- Michael E J Buhl
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Nuremberg, Germany
| | - Jan P Meier-Kolthoff
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Matthias Marschal
- Institute of Medical Microbiology and Hygiene, Tübingen University Hospital, Tübingen, Germany
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Non-oral Prevotella stepping into the spotlight. Anaerobe 2021; 68:102321. [PMID: 33482304 DOI: 10.1016/j.anaerobe.2021.102321] [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: 08/25/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 02/07/2023]
Abstract
Species now affiliated to genus Prevotella have been known for decades as an integral part of human oral cavity microbiota. They were frequently isolated from patients with periodontitis or from dental root canals but also from healthy subjects. With the exception of Prevotella intermedia, they were considered opportunistic pathogens, as they were isolated also from various bacterial abscesses from the head, neck, breast, skin and various other body sites. Consequently, Prevotella were not in the focus of research activities. On the other hand, the four species found in the rumen never caused any disease and seemed early on to be numerous and important part of the rumen ecosystem indicating this genus harbored bacteria with enormously diverse habitats and lifestyles. The purpose of this review is to illustrate the main research themes performed in Prevotella on a path from less noted oral bacteria and from hard to cultivate and study rumen organisms to important mutualistic bacteria in guts of various mammals warranting major research efforts.
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Buhl M, Dunlap C, Marschal M. Prevotella brunnea sp. nov., isolated from a wound of a patient. Int J Syst Evol Microbiol 2019; 69:3933-3938. [PMID: 31644420 DOI: 10.1099/ijsem.0.003715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A strain of an obligately anaerobic, Gram-stain-negative rod-shaped bacterium is described by phenotypical, biochemical and genotypical characterization. Strain A2672T was isolated from a wound of a patient sampled during routine care at hospital. Phylogenetic analysis was based on full-length 16S rRNA gene sequence analysis and revealed the strain to belong to the genus Prevotella, but to be distant from known species, with the closest relationship to Prevotella corporis. The genomic DNA G+C content was 44.0 mol%. Strain A2672T was moderately saccharolytic and proteolytic. The most abundant cellular long-chain fatty acids were anteiso-C15 : 0 and iso-C15 : 0. In view of these characteristics as well as whole-genome sequence analysis, strain A2672T is considered to represent a novel species within the genus Prevotella, for which the name Prevotella brunnea sp. nov. is proposed. The type strain is A2672T (=DSM 108033T=CCOS 1231T=CCUG 72809T).
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Affiliation(s)
- Michael Buhl
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Christopher Dunlap
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, Illinois, USA
| | - Matthias Marschal
- Institute of Medical Microbiology and Hygiene, Tübingen University Hospital, Tübingen, Germany
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Efimov B, Chaplin A, Sokolova S, Chernaia Z, Pikina A, Savilova A, Kafarskaya L. Application of culture-based, mass spectrometry and molecular methods to the study of gut microbiota in children. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In recent decades, nucleic acid sequencing technologies used for metagenomic analysis have become the main methods for assessing the composition of microbiota. At the same time, the use of novel methods of cultivation and identification of microorganisms in microbiological research led to the renaissance of culture-based technologies, because facilitated the discovery and isolation of both new strains of well-known microorganisms as well as uncultivated and unexplored bacterial taxa. The aim of this study was to evaluate the potential of using the culture-based method for the assessment of the qualitative and quantitative composition of the intestinal microbiota in healthy children. Eleven growth media were inoculated with serial dilutions of stool samples in order to analyze the profile of dominant anaerobic bacteria, as well as aerobic bacteria and fungi in 20 healthy children aged 2–4 years. The identification of microorganisms was performed using MALDI TOF MS and 16S rRNA gene fragment sequencing were used. 1,819 isolated and identified strains belong to 7 phyla, 13 classes, 18 orders, 33 families, 77 genera and 149 species in the Bacteria domain. The Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria phyla were most abundant and frequent. The greatest species diversity (more than 85 species) was found in the Firmicutes phylum. Ten new previously uncharacterized bacterial strains were isolated.
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Affiliation(s)
- B.A. Efimov
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - A.V. Chaplin
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - S.R. Sokolova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Z.A. Chernaia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - A.P. Pikina
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - A.M. Savilova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - L.I. Kafarskaya
- Pirogov Russian National Research Medical University, Moscow, Russia
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