Analysis of the Composition of Lactobacilli in Humans
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The Significance of Lactobacillus Crispatus and L. Vaginalis for Vaginal Health and the Negative Effect of Recent
Jespers et al. BMC Infectious Diseases (2015) 15:115 DOI 10.1186/s12879-015-0825-z RESEARCH ARTICLE Open Access The significance of Lactobacillus crispatus and L. vaginalis for vaginal health and the negative effect of recent sex: a cross-sectional descriptive study across groups of African women Vicky Jespers1*, Janneke van de Wijgert2, Piet Cools3, Rita Verhelst4, Hans Verstraelen5, Sinead Delany-Moretlwe6, Mary Mwaura7, Gilles F Ndayisaba8, Kishor Mandaliya7, Joris Menten9, Liselotte Hardy1,10, Tania Crucitti10 and for the Vaginal Biomarkers Study Group Abstract Background: Women in sub-Saharan Africa are vulnerable to acquiring HIV infection and reproductive tract infections. Bacterial vaginosis (BV), a disruption of the vaginal microbiota, has been shown to be strongly associated with HIV infection. Risk factors related to potentially protective or harmful microbiota species are not known. Methods: We present cross-sectional quantitative polymerase chain reaction data of the Lactobacillus genus, five Lactobacillus species, and three BV-related bacteria (Gardnerella vaginalis, Atopobium vaginae,andPrevotella bivia) together with Escherichia coli and Candida albicans in 426 African women across different groups at risk for HIV. We selected a reference group of adult HIV-negative women at average risk for HIV acquisition and compared species variations in subgroups of adolescents, HIV-negative pregnant women, women engaging in traditional vaginal practices, sex workers and a group of HIV-positive women on combination antiretroviral therapy. We explored the associations between presence and quantity of the bacteria with BV by Nugent score, in relation to several factors of known or theoretical importance. Results: The presence of species across Kenyan, South African and Rwandan women was remarkably similar and few differences were seen between the two groups of reference women in Kenya and South Africa. -
The Histidine Decarboxylase Gene Cluster of Lactobacillus Parabuchneri Was Gained by Horizontal Gene Transfer and Is Mobile Within the Species
ORIGINAL RESEARCH published: 17 February 2017 doi: 10.3389/fmicb.2017.00218 The Histidine Decarboxylase Gene Cluster of Lactobacillus parabuchneri Was Gained by Horizontal Gene Transfer and Is Mobile within the Species Daniel Wüthrich 1, Hélène Berthoud 2, Daniel Wechsler 2, Elisabeth Eugster 2, Stefan Irmler 2 and Rémy Bruggmann 1* 1 Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland, 2 Agroscope, Institute for Food Sciences, Bern, Switzerland Histamine in food can cause intolerance reactions in consumers. Lactobacillus parabuchneri (L. parabuchneri) is one of the major causes of elevated histamine levels in cheese. Despite its significant economic impact and negative influence on human health, no genomic study has been published so far. We sequenced and Edited by: analyzed 18 L. parabuchneri strains of which 12 were histamine positive and 6 were Danilo Ercolini, histamine negative. We determined the complete genome of the histamine positive strain University of Naples Federico II, Italy FAM21731 with PacBio as well as Illumina and the genomes of the remaining 17 strains Reviewed by: using the Illumina technology. We developed the synteny aware ortholog finding algorithm Patrick Lucas, University of Bordeaux 1, France SynOrf to compare the genomes and we show that the histidine decarboxylase (HDC) Daniel M. Linares, gene cluster is located in a genomic island. It is very likely that the HDC gene cluster Teagasc - The Irish Agriculture and Food Development Authority, Ireland was transferred from other lactobacilli, as it is highly conserved within several lactobacilli *Correspondence: species. Furthermore, we have evidence that the HDC gene cluster was transferred within Rémy Bruggmann the L. -
A Taxonomic Note on the Genus Lactobacillus
Taxonomic Description template 1 A taxonomic note on the genus Lactobacillus: 2 Description of 23 novel genera, emended description 3 of the genus Lactobacillus Beijerinck 1901, and union 4 of Lactobacillaceae and Leuconostocaceae 5 Jinshui Zheng1, $, Stijn Wittouck2, $, Elisa Salvetti3, $, Charles M.A.P. Franz4, Hugh M.B. Harris5, Paola 6 Mattarelli6, Paul W. O’Toole5, Bruno Pot7, Peter Vandamme8, Jens Walter9, 10, Koichi Watanabe11, 12, 7 Sander Wuyts2, Giovanna E. Felis3, #*, Michael G. Gänzle9, 13#*, Sarah Lebeer2 # 8 '© [Jinshui Zheng, Stijn Wittouck, Elisa Salvetti, Charles M.A.P. Franz, Hugh M.B. Harris, Paola 9 Mattarelli, Paul W. O’Toole, Bruno Pot, Peter Vandamme, Jens Walter, Koichi Watanabe, Sander 10 Wuyts, Giovanna E. Felis, Michael G. Gänzle, Sarah Lebeer]. 11 The definitive peer reviewed, edited version of this article is published in International Journal of 12 Systematic and Evolutionary Microbiology, https://doi.org/10.1099/ijsem.0.004107 13 1Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key 14 Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, P.R. China. 15 2Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience 16 Engineering, University of Antwerp, Antwerp, Belgium 17 3 Dept. of Biotechnology, University of Verona, Verona, Italy 18 4 Max Rubner‐Institut, Department of Microbiology and Biotechnology, Kiel, Germany 19 5 School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland 20 6 University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy 21 7 Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit 22 Brussel, Brussels, Belgium 23 8 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, 24 Belgium 25 9 Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada 26 10 Department of Biological Sciences, University of Alberta, Edmonton, Canada 27 11 National Taiwan University, Dept. -
Microbial Community Dynamics In
Microbial community dynamics in traditionally fermented milk PhD thesis Anneloes E Groenenboom Wageningen University and Research 2 Table of contents Chapter 1. Introduction 5 Chapter 2. Microbial communities from spontaneously fermented foods as model system to study eco-evolutionary dynamics 13 Chapter 3. Robust sampling and preservation of DNA for microbial community profiling in field experiments 25 Chapter 4. Microbial population dynamics during traditional production of Mabisi, a spontaneously fermented milk product from Zambia. A field trial. 33 Chapter 5. Does change in bacterial species composition of natural communities reflect adaptation to a new environment? 49 Chapter 6. Bacterial community dynamics in Lait caillé, a traditional product of spontaneous fermentation from Senegal. 65 Chapter 7. General discussion 79 Summary 91 References 95 3 4 1. Introduction This thesis is about Mabisi. In the western world, and maybe anywhere but Zambia, Mabisi is an unknown product. In this country in the middle of Africa, however, Mabisi is a phenomenon; a widely appreciated fermented milk product, which is consumed almost daily by men, women, and children from a very young age. What makes this fermented milk so interesting that I studied it for four years? It is the diversity we find in the bacterial communities that make Mabisi. This PhD thesis is part of a larger project funded by NWO WOTRO on enhancing nutrition security though traditional fermented products (1). In this thesis I would like to show the microbial communities that are responsible for the fermentation and how we can use the constituting bacteria to learn about bacterial community dynamics over time. -
Evaluation of Commercially Available Probiotic Products Intended for Children in the Republic of the Philippines and the Republic of Korea
foods Article Do Your Kids Get What You Paid for? Evaluation of Commercially Available Probiotic Products Intended for Children in the Republic of the Philippines and the Republic of Korea Clarizza May Dioso 1,2, Pierangeli Vital 3, Karina Arellano 2, Haryung Park 2,4, Svetoslav Dimitrov Todorov 2, Yosep Ji 4 and Wilhelm Holzapfel 2,4,* 1 Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines; [email protected] 2 Advanced Green Energy and Environment Department, Handong Global University, Pohang, Gyungbuk 37554, Korea; [email protected] (K.A.); [email protected] (H.P.); [email protected] (S.D.T.) 3 Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; [email protected] 4 HEM Inc., Business Incubator, Handong Global University, Pohang, Gyungbuk 37554, Korea; [email protected] * Correspondence: [email protected]; Tel.: +82-20-8455-1360 Received: 11 August 2020; Accepted: 31 August 2020; Published: 3 September 2020 Abstract: A wide range of probiotic products is available on the market and can be easily purchased over the counter and unlike pharmaceutical drugs, their commercial distribution is not strictly regulated. In this study, ten probiotic preparations commercially available for children’s consumption in the Republic of the Philippines (PH) and the Republic of Korea (SK) have been investigated. The analyses included determination of viable counts and taxonomic identification of the bacterial species present in each formulation. The status of each product was assessed by comparing the results with information and claims provided on the label. In addition to their molecular identification, safety assessment of the isolated strains was conducted by testing for hemolysis, biogenic amine production and antibiotic resistance. -
Comparative Genomics Analysis of Lactobacillus Mucosae from Different Niches
G C A T T A C G G C A T genes Article Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches Yan Jia 1,2, Bo Yang 1,2,3,* , Paul Ross 3,4, Catherine Stanton 3,5, Hao Zhang 1,2,6,7, Jianxin Zhao 1,2,6 and Wei Chen 1,2,6,8 1 State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; [email protected] (Y.J.); [email protected] (H.Z.); [email protected] (J.Z.); [email protected] (W.C.) 2 School of Food Science and Technology, Jiangnan University, Wuxi 214122, China 3 International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China; [email protected] (P.R.); [email protected] (C.S.) 4 APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland 5 Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland 6 National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China 7 Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China 8 Beijing Innovation Center of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 102488, China * Correspondence: [email protected]; Tel.: +86-510-591-2155 Received: 5 December 2019; Accepted: 9 January 2020; Published: 14 January 2020 Abstract: The potential probiotic benefits of Lactobacillus mucosae have received increasing attention. To investigate the genetic diversity of L. mucosae, comparative genomic analyses of 93 strains isolated from different niches (human and animal gut, human vagina, etc.) and eight strains of published genomes were conducted. -
Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria
Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria Sujatha Srinivasan1*, Noah G. Hoffman2, Martin T. Morgan3, Frederick A. Matsen3, Tina L. Fiedler1, Robert W. Hall4, Frederick J. Ross3, Connor O. McCoy3, Roger Bumgarner4, Jeanne M. Marrazzo5, David N. Fredricks1,4,5* 1 Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America, 2 Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America, 3 Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America, 4 Department of Microbiology, University of Washington, Seattle, Washington, United States of America, 5 Department of Medicine, University of Washington, Seattle, Washington, United States of America Abstract Background: Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV. Methodology/Principal Findings: Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel’s clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. -
Multi-Strain Probiotics: Synergy Among Isolates Enhances Biological Activities
biology Review Multi-Strain Probiotics: Synergy among Isolates Enhances Biological Activities Iliya D. Kwoji 1, Olayinka A. Aiyegoro 2,3 , Moses Okpeku 1 and Matthew A. Adeleke 1,* 1 Discipline of Genetics, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Durban 4000, South Africa; [email protected] (I.D.K.); [email protected] (M.O.) 2 Gastrointestinal Microbiology and Biotechnology Unit, Agricultural Research Council-Animal Production, Irene 0062, South Africa; [email protected] 3 Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa * Correspondence: [email protected] Simple Summary: Multi-strain probiotics are composed of more than one species or strains of bacteria and sometimes, including some fungal species with benefits to human and animals’ health. The mechanisms by which multi-strain probiotics exert their effects include cell–cell communications, interactions with the host tissues, and modulation of the immune systems. Multi-strain probiotics applications include alleviation of disease conditions, inhibition of pathogens, and restoration of the gastrointestinal microbiome. Despite all these benefits, the potential of using multi-strain probiotics is still not fully explored. Abstract: The use of probiotics for health benefits is becoming popular because of the quest for safer products with protective and therapeutic effects against diseases and infectious agents. The emergence and spread of antimicrobial resistance among pathogens had prompted restrictions over Citation: Kwoji, I.D.; Aiyegoro, O.A.; the non-therapeutic use of antibiotics for prophylaxis and growth promotion, especially in animal Okpeku, M.; Adeleke, M.A. husbandry. While single-strain probiotics are beneficial to health, multi-strain probiotics might be Multi-Strain Probiotics: Synergy among Isolates Enhances Biological more helpful because of synergy and additive effects among the individual isolates. -
A Taxonomic Note on the Genus Lactobacillus
TAXONOMIC DESCRIPTION Zheng et al., Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.004107 A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae Jinshui Zheng1†, Stijn Wittouck2†, Elisa Salvetti3†, Charles M.A.P. Franz4, Hugh M.B. Harris5, Paola Mattarelli6, Paul W. O’Toole5, Bruno Pot7, Peter Vandamme8, Jens Walter9,10, Koichi Watanabe11,12, Sander Wuyts2, Giovanna E. Felis3,*,†, Michael G. Gänzle9,13,*,† and Sarah Lebeer2† Abstract The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and gen- otypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade- specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host- adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacil- lus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, -
The Human Vaginal Microbial Community
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Ghent University Academic Bibliography Research in Microbiology 168 (2017) 811e825 www.elsevier.com/locate/resmic The human vaginal microbial community Mario Vaneechoutte Laboratory for Bacteriology Research, Ghent University, MRB2, De Pintelaan 185, 9000 Gent, Belgium Received 14 June 2017; accepted 16 August 2017 Available online 26 August 2017 Abstract Monopolization of the vaginal econiche by a limited number of Lactobacillus species, resulting in low pH of 3.5e4.5, has been shown to protect women against vaginal dysbiosis, sexually transmitted infections and adverse pregnancy outcomes. Still, controversy exists as to which characteristics of lactobacilli are most important with regard to colonization resistance and to providing protection. This review addresses the antimicrobial and anti-inflammatory roles of lactic acid (and low pH) and hydrogen peroxide (and oxidative stress) as means of lactobacilli to dominate the vaginal econiche. © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved. Keywords: Vagina; Glycogen; Lactobacilli; Lactic acid; Hydrogen peroxide 1. Definition and dynamics of the normal vaginal against sexually transmitted infections (STIs) and adverse microbial community pregnancy outcome (APO). In other words, the mere absence of these probiotic bacteria from the vaginal econiche is a 1.1. What is normal? health risk factor for women, their partners and their unborn and new-born children. Moreover, it is becoming clear that it It has recently been claimed that almost any type of vaginal is especially lactic acid [4,5], and probably even more, D-lactic microbial community (VMC) can be considered as normal, acid, as produced by only some vaginal lactobacilli [6], but not since even in the absence of lactobacilli there is frequently a any organic acid, that are health-promoting. -
Lactobacillus Mucosae and Bifidobacterium Longum
J. Microbiol. Biotechnol. (2019), 29(9), 1369–1374 https://doi.org/10.4014/jmb.1907.07044 Research Article Review jmb Lactobacillus mucosae and Bifidobacterium longum Synergistically Alleviate Immobilization Stress-Induced Anxiety/Depression in Mice by Suppressing Gut Dysbiosis S Sang-Kap Han and Dong-Hyun Kim* Neurobiota Research Center, Department of Life and Nanopharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea Received: July 21, 2019 Revised: August 13, 2019 We isolated Lactobacillus mucosae NK41 and Bifidobacterium longum NK46 from human feces, Accepted: August 15, 2019 which induced BDNF expression in corticosterone-stimulated SH-SY5Y cells, and examined First published online their anti-depressive effects in mice. NK41, NK46, and their (1:1) mixture significantly August 21, 2019 mitigated immobilization stress (IS)-induced anxiety-like/depressive behaviors, hippocampal + *Corresponding author NF-κB activation, BDNF expression, Iba1 cell population, and blood corticosterone, TNF-α, IL- Phone: +82-2-961-0374; 6, and lipopolysaccharide levels. Furthermore, they inhibited colitis marker NF-κB activation, Fax: +82-2-957-5030; E-mail: [email protected] and TNF-α expression in mice with IS-induced anxiety/depression. They additionally suppressed gut Proteobacteria and Bacteroidetes populations and bacterial lipopolysaccharide S upplementary data for this production. These findings suggest that NK41 and NK46 may alleviate anxiety/depression paper are available on-line only at http://jmb.or.kr. and colitis by suppressing gut dysbiosis. pISSN 1017-7825, eISSN 1738-8872 Keywords: Bifidobacterium longum, Lactobacillus mucosae, depression, anxiety, gut microbiota Copyright© 2019 by The Korean Society for Microbiology and Biotechnology Anxiety disorders are the most commonly reported bifidobacteria and lactobacilli alleviated psychiatric mental disorders [1]. -
Amplicon Sequencing of the Slph Locus Permits Culture-Independent Strain Typing of Lactobacillus Helveticus in Dairy Products
ORIGINAL RESEARCH published: 20 July 2017 doi: 10.3389/fmicb.2017.01380 Amplicon Sequencing of the slpH Locus Permits Culture-Independent Strain Typing of Lactobacillus helveticus in Dairy Products Aline Moser 1, 2, Daniel Wüthrich 3, Rémy Bruggmann 3, Elisabeth Eugster-Meier 4, Leo Meile 2 and Stefan Irmler 1* 1 Agroscope, Bern, Switzerland, 2 Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland, 3 Interfaculty Bioinformatics Unit, University of Bern and Swiss Institute of Bioinformatics, Bern, Switzerland, 4 School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland The advent of massive parallel sequencing technologies has opened up possibilities for the study of the bacterial diversity of ecosystems without the need for enrichment or single strain isolation. By exploiting 78 genome data-sets from Lactobacillus helveticus strains, we found that the slpH locus that encodes a putative surface layer protein displays sufficient genetic heterogeneity to be a suitable target for strain typing. Based on Edited by: high-throughput slpH gene sequencing and the detection of single-base DNA sequence Danilo Ercolini, University of Naples Federico II, Italy variations, we established a culture-independent method to assess the biodiversity of Reviewed by: the L. helveticus strains present in fermented dairy food. When we applied the method Pierre Renault, to study the L. helveticus strain composition in 15 natural whey cultures (NWCs) that Institut National de la Recherche Agronomique (INRA), France were collected at different Gruyère, a protected designation of origin (PDO) production Monica Gatti, facilities, we detected a total of 10 sequence types (STs).