101
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Ahn Y, Jung JY, Kweon O, Veach BT, Khare S, Gokulan K, Piñeiro SA, Cerniglia CE. Impact of Chronic Tetracycline Exposure on Human Intestinal Microbiota in a Continuous Flow Bioreactor Model. Antibiotics (Basel) 2021; 10:antibiotics10080886. [PMID: 34438936 PMCID: PMC8388752 DOI: 10.3390/antibiotics10080886] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 01/02/2023] Open
Abstract
Studying potential dietary exposure to antimicrobial drug residues via meat and dairy products is essential to ensure human health and consumer safety. When studying how antimicrobial residues in food impact the development of antimicrobial drug resistance and disrupt normal bacteria community structure in the intestine, there are diverse methodological challenges to overcome. In this study, traditional cultures and molecular analysis techniques were used to determine the effects of tetracycline at chronic subinhibitory exposure levels on human intestinal microbiota using an in vitro continuous flow bioreactor. Six bioreactor culture vessels containing human fecal suspensions were maintained at 37 °C for 7 days. After a steady state was achieved, the suspensions were dosed with 0, 0.015, 0.15, 1.5, 15, or 150 µg/mL tetracycline, respectively. Exposure to 150 µg/mL tetracycline resulted in a decrease of total anaerobic bacteria from 1.9 × 107 ± 0.3 × 107 down to 2 × 106 ± 0.8 × 106 CFU/mL. Dose-dependent effects of tetracycline were noted for perturbations of tetB and tetD gene expression and changes in acetate and propionate concentrations. Although no-observed-adverse-effect concentrations differed, depending on the traditional cultures and the molecular analysis techniques used, this in vitro continuous flow bioreactor study contributes to the knowledge base regarding the impact of chronic exposure of tetracycline on human intestinal microbiota.
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Affiliation(s)
- Youngbeom Ahn
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (J.Y.J.); (O.K.); (S.K.); (K.G.); (C.E.C.)
- Correspondence: ; Tel.: +1-870-540-7084
| | - Ji Young Jung
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (J.Y.J.); (O.K.); (S.K.); (K.G.); (C.E.C.)
| | - Ohgew Kweon
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (J.Y.J.); (O.K.); (S.K.); (K.G.); (C.E.C.)
| | - Brian T. Veach
- Office of Regulatory Affairs, Arkansas Laboratory, U.S. Food and Drug Administration, Jefferson, AR 72079, USA;
| | - Sangeeta Khare
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (J.Y.J.); (O.K.); (S.K.); (K.G.); (C.E.C.)
| | - Kuppan Gokulan
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (J.Y.J.); (O.K.); (S.K.); (K.G.); (C.E.C.)
| | - Silvia A. Piñeiro
- Division of Human Food Safety, Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, MD 72079, USA;
| | - Carl E. Cerniglia
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (J.Y.J.); (O.K.); (S.K.); (K.G.); (C.E.C.)
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102
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Junkins EN, Stevenson BS. Using Plate-Wash PCR and High-Throughput Sequencing to Measure Cultivated Diversity for Natural Product Discovery Efforts. Front Microbiol 2021; 12:675798. [PMID: 34354680 PMCID: PMC8329497 DOI: 10.3389/fmicb.2021.675798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/28/2021] [Indexed: 12/16/2022] Open
Abstract
Molecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Sequence-based data indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete and more complex, understanding of which organisms were present compared to what was eventually detected during cultivation. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against an already multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.
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Affiliation(s)
- Emily N Junkins
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Bradley S Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
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103
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Campisciano G, Quadrifoglio M, Comar M, De Seta F, Zanotta N, Ottaviani C, Barbieri M, Chiodo A, Stampalija T. Evidence of bacterial DNA presence in chorionic villi and amniotic fluid in the first and second trimester of pregnancy. Future Microbiol 2021; 16:801-810. [PMID: 34223788 DOI: 10.2217/fmb-2020-0243] [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: 01/02/2023] Open
Abstract
The sterile-womb dogma in uncomplicated pregnancy has been lively debated. Data regarding the in utero microbiome environment are based mainly on studies performed at the time of delivery. Aim: To determine whether human placenta and amniotic fluid are populated by a bacterial microbiota in the first and second trimesters of pregnancy. Materials & methods: We analyzed by next-generation sequencing method 24 and 29 samples from chorionic villus sampling (CVS) and amniocentesis (AC), respectively. The V3 region of the 16S rRNA gene was sequenced. Results: 37.5% of CVS and 14% of AC samples showed the presence of bacterial DNA. Conclusion: Our study suggests that bacterial DNA can be identified in the placenta and amniotic fluid during early prenatal life.
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Affiliation(s)
- Giuseppina Campisciano
- Unit of Advanced Microbiology Diagnosis & Translational Research, Institute for Maternal & Child Health, IRCCS Burlo Garofolo, Via dell'Istria 65/1, Trieste, 34137, Italy
| | - Mariachiara Quadrifoglio
- Unit of Fetal Medicine & Prenatal Diagnosis, Institute for Maternal & Child Health, IRCCS Burlo Garofolo, Via dell'Istria 65/1, Trieste, 34137, Italy
| | - Manola Comar
- Unit of Advanced Microbiology Diagnosis & Translational Research, Institute for Maternal & Child Health, IRCCS Burlo Garofolo, Via dell'Istria 65/1, Trieste, 34137, Italy
| | - Francesco De Seta
- Department of Medical, Surgical & Health Sciences, University of Trieste, Strada di Fiume 447, Trieste, 34149, Italy.,Obstetrics & Gynecology, Institute for Maternal & Child Health, IRCCS Burlo Garofolo, Via dell'Istria 65/1, Trieste, 34137, Italy
| | - Nunzia Zanotta
- Unit of Advanced Microbiology Diagnosis & Translational Research, Institute for Maternal & Child Health, IRCCS Burlo Garofolo, Via dell'Istria 65/1, Trieste, 34137, Italy
| | - Chiara Ottaviani
- Department of Medical, Surgical & Health Sciences, University of Trieste, Strada di Fiume 447, Trieste, 34149, Italy
| | - Moira Barbieri
- Unit of Fetal Medicine & Prenatal Diagnosis, Institute for Maternal & Child Health, IRCCS Burlo Garofolo, Via dell'Istria 65/1, Trieste, 34137, Italy
| | - Antonella Chiodo
- Department of Obstetrics & Gynecology, Policlinico Universitario Duilio Casula, University of Cagliari, SS 554, 09042 Monserrato, Cagliari, Italy
| | - Tamara Stampalija
- Unit of Fetal Medicine & Prenatal Diagnosis, Institute for Maternal & Child Health, IRCCS Burlo Garofolo, Via dell'Istria 65/1, Trieste, 34137, Italy.,Department of Medical, Surgical & Health Sciences, University of Trieste, Strada di Fiume 447, Trieste, 34149, Italy
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104
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Sarr M, Diouf FS, Lo CI, Tidjani Alou M, Alibar S, Million M, Sokhna C, Fenollar F. Taxonogenomics description of Bacillus marasmi sp. nov., a new species isolated from the stool sample. New Microbes New Infect 2021; 42:100906. [PMID: 34188938 PMCID: PMC8220230 DOI: 10.1016/j.nmni.2021.100906] [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: 03/02/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/05/2022] Open
Abstract
Using the culturomics method, two strains were isolated, identified, and characterised following the taxonogenomics concept. Bacillus marasmi sp. nov. strain Marseille-P3556 (= CSURP3556) is isolated from a 13-month-old girl living in Niger. The phylogenetic tree, phenotypic criteria, and genomic analysis described here clearly show that this bacterium is different from previously known bacterial species withstanding in nomenclature and new members of Bacillus genus.
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Affiliation(s)
- M Sarr
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - F S Diouf
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - M Tidjani Alou
- 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
| | - C Sokhna
- IHU-Méditerranée Infection, Marseille, France.,Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - F Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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105
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Townsend EM, Kelly L, Muscatt G, Box JD, Hargraves N, Lilley D, Jameson E. The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. Front Cell Infect Microbiol 2021; 11:643214. [PMID: 34150671 PMCID: PMC8213399 DOI: 10.3389/fcimb.2021.643214] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.
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Affiliation(s)
- Eleanor M Townsend
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Lucy Kelly
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - George Muscatt
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Joshua D Box
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Nicole Hargraves
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Daniel Lilley
- Warwick Medical School, The University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
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106
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Zgheib R, Anani H, Meng MM, Mailhe M, Ricaboni D, Morand A, Caputo A, Traore SI, Fontanini A, Armstrong N, Raoult D, Fournier PE. New human-associated species of the family Atopobiaceae and proposal to reclassify members of the genus Olsenella. Int J Syst Evol Microbiol 2021; 71. [PMID: 34047688 DOI: 10.1099/ijsem.0.004819] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Five novel bacterial strains, Marseille-P1476T (=CSURP1476T=DSM 100642T), Marseille-P3256T (=CSURP3256T=CECT 9977T), Marseille-P2936T (=CSURP2936T=DSM 103159T), Marseille-P2912T (=CSURP2912T=DSM 103345T) and Marseille-P3197T (=CSURP3197T=CCUG 71847T), were isolated from various human specimens. These five strains were not identified at the species level by matrix-assisted laser desorption/ionization time of flight mass spectrometry. Following 16S rRNA gene sequence comparisons with the GenBank database, the highest nucleotide sequence similarities of all studied strains were obtained to members of the paraphyletic genus Olsenella. A polyphasic taxono-genomic strategy (16S rRNA gene-based and core genome-based phylogeny, genomic comparison, phenotypic and biochemical characteristics) enabled us to better classify these strains and reclassify Olsenella species. Among the studied strains, Marseille-P1476T, Marseille-P2936T and Marseille-P3197T belonged to new species of the genus Olsenella for which we propose the names Olsenella massiliensis sp. nov., Olsenella phocaeensis sp. nov. and Olsenella urininfantis sp. nov., respectively. Strains Marseille-P2912T and Marseille-P3256T belonged to a new genus for which the names Thermophilibacter provencensis gen. nov., sp. nov. and Thermophilibacter mediterraneus gen. nov., sp. nov. are proposed, respectively. We also propose the creation of the genera Parafannyhessea gen. nov., Tractidigestivibacter gen. nov. and Paratractidigestivibacter gen. nov. and the reclassification of Olsenella umbonata as Parafannyhessea umbonata comb. nov., Olsenella scatoligenes as Tractidigestivibacter scatoligenes comb. nov., and Olsenella faecalis as Paratractidigestivibacter faecalis comb. nov.
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Affiliation(s)
- Rita Zgheib
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Hussein Anani
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Marine Makoa Meng
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Morgane Mailhe
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Davide Ricaboni
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Aurélie Morand
- Pédiatrie spécialisée et médecine infantile, Hôpital de la Timone, AP-HM, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Aurelia Caputo
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sory Ibrahima Traore
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Anthony Fontanini
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Pierre Edouard Fournier
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
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107
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Gu Y, Yan D, Wu M, Li M, Li P, Wang J, Chang Y, Yang F, Di S, Ni S, Yang M, Liu J. Influence of the densities and nutritional components of bacterial colonies on the culture-enriched gut bacterial community structure. AMB Express 2021; 11:78. [PMID: 34057622 PMCID: PMC8167003 DOI: 10.1186/s13568-021-01240-6] [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: 01/03/2021] [Accepted: 05/24/2021] [Indexed: 11/10/2022] Open
Abstract
Isolating relevant microorganisms is still a substantial challenge that limits the use of bacteria in the maintenance of human health. To confirm which media and which bacterial colony densities can enrich certain kinds of bacteria, we selected eight common media and used them to enrich the gut microorganisms on agar plates. Then, we calculated the numbers of bacterial colonies and collected the bacterial culture mixtures from each kind of medium. Using the Illumina HiSeq platform, we analyzed the composition and diversity of the culture-enriched gut bacterial community. Our data suggested that medium supplemented with blood could increase the diversity of the bacterial community. In addition, beef powder and peptone could significantly change the culture-enriched bacterial community. A moderate density (100-150 colony-forming units per plate) was optimal for obtaining the highest diversity on the agar. Similarly, membrane transport was significantly enriched in the moderate-density group, which indicated a more active metabolism in this density range. Overall, these results reveal the optimal culture conditions, including the densities of colonies and nutritional components for various gut bacteria, that provide a novel strategy for isolating bacteria in a way that is targeted and avoids blinded and repetitive work.
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108
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Traore SI, Lo CI, Bilen M, Raoult D, Fenollar F, Fournier PE. Lagierella massiliensis gen. nov., sp. nov., Isolated from a Stool Sample. Curr Microbiol 2021; 78:2481-2487. [PMID: 34043027 DOI: 10.1007/s00284-021-02539-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Strain Marseille-P2012T was described to represent a new bacterial genus belonging to the phylum Firmicutes using the taxonogenomics concept. It was isolated from stool samples of a healthy 2-year-old Senegalese boy in a study of the human gut microbiota. This strain is a Gram-positive, anaerobic, non-motile and coccus-shaped bacterium. The 16S rRNA gene sequence of strain Marseille-P2012 exhibited 90.5% similarity with Finegoldia magna strain ATCC 29,328, the phylogenetically closest species with standing in nomenclature. The genome of strain Marseille-P2012T is 1,832,315 bp-long with 32.46 mol% of G + C content. With regard to its phenotypic, biochemical and genomic characteristics, this bacterium was classified as a new bacterial genus and species, Lagierella massiliensis gen. nov., sp. nov., with strain Marseille-P2012T (= CSUR P2012 = DSM100854) as type strain.
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Affiliation(s)
- Sory Ibrahima Traore
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, cedex 05, Marseille, France
| | - Melhem Bilen
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Florence Fenollar
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, cedex 05, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France. .,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, cedex 05, Marseille, France.
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109
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Khare M, Sinha D, Zgheib R, Traore SI, Lagier JC, Raoult D, Edouard FP. Genomic description and characterization of Nigeribacterium massiliense gen. nov., sp. nov., isolated from the human gut. Microbes Infect 2021; 23:104842. [PMID: 34020025 DOI: 10.1016/j.micinf.2021.104842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/23/2021] [Accepted: 05/08/2021] [Indexed: 02/07/2023]
Abstract
Strain Marseille-P1302 was isolated from the stool of a 2-year-old Nigerian boy suffering from Kwashiorkor, a form of severe acute malnutrition. The strain grows in aerobic atmosphere and bacterial cells are Gram-positive cocci ranging in diameter from 0.8 to 1 μm. Strain Marseille-P1302 exhibits a 16S rRNA sequence similarity of 94.97% with Brevilactibacter flavus strain VG341T, but phylogenetically-closest species with standing in nomenclature is Brevilactibacter sinopodophylli strains KCTC 33808Twith the sequence similarity of 93.41%. The draft genome of strain Marseille-P1302 is 2,934,258bp-long with a 70.38% G+C content, and contains 2,704 protein-coding genes and 55 RNAs that includes 9 rRNA genes. On the basis of these data, we propose the creation of the new genus Nigeribacterium gen. nov., with strain Marseille-P1302T (= CSUR P1302 = DSM 29084) being the type strain of new species Nigeribacterium. massiliense gen. nov., sp. nov.
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Affiliation(s)
- Mudra Khare
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Dhiraj Sinha
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Rita Zgheib
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Sory Ibrahima Traore
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Jean-Christophe Lagier
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Fournier Pierre Edouard
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
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Wongkuna S, Ghimire S, Chankhamhaengdecha S, Janvilisri T, Scaria J. Description of Collinsella avium sp. nov., a new member of the Collinsella genus isolated from the ceacum of feral chicken. New Microbes New Infect 2021; 42:100902. [PMID: 34168883 PMCID: PMC8207210 DOI: 10.1016/j.nmni.2021.100902] [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: 08/21/2020] [Revised: 04/19/2021] [Accepted: 05/09/2021] [Indexed: 11/17/2022] Open
Abstract
An obligately anaerobic, non-motile and Gram-positive rod bacterium, strain SW219 was isolated from ceacum of feral chickens. Based on 16S rRNA sequence analysis, the strain SW219 exhibited 97.88% similarity to Collinsella massiliensis strain GD3 strain, the closest valid species. The genome size of SW219 was 2.58 Mbp with 64.5 mol% of G+C content. The phenotypic and genotypic analysis suggested that the strain SW219 is a new species belonging to the family Coriobacteriaceae within the Actinobacteria phylum, which the name Collinsella avium sp. nov. is proposed. The type strain of Collinsella avium is SW219 (= DSM 109235T and = CCOS 1884T).
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Affiliation(s)
- S. Wongkuna
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
- South Dakota Center for Biologics Research and Commercialization, SD, USA
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - S. Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
- South Dakota Center for Biologics Research and Commercialization, SD, USA
| | | | - T. Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - J. Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
- South Dakota Center for Biologics Research and Commercialization, SD, USA
- Corresponding author: J. Scaria, Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
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111
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Singh D, Gupta S. Butyrate: A Review on Beneficial Pharmacological and Therapeutic Effect. CURRENT NUTRITION & FOOD SCIENCE 2021. [DOI: 10.2174/1573401316999201029210912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background::
Short-chain fatty acids (SCFAs), generally acetate, propionate along with
butyrate, are aliphatic organic acids formed in the gut mucosa through bacterial fermentation of
mostly undigested nutritional carbohydrates, again to a minor degree by natural and dietary proteins,
such as mucous and shed epithelial cells.
Methods::
Many sources were used to collect information about Butyrate, such as Pub med, Google
Scholar, Pubmed, Scopus and other reliable sources.
:
Endogenous butyrate formation, absorption, and transportation by colon cells have now been well
acknowledged. Butyrate exerts its action features by way of appearing as a histone deacetylase inhibitor,
even signaling through a few protein receptors. Lately, butyrate has received special consideration
for its favorable result on intestinal equilibrium and also energy metabolism. There is a
growing interest in butyrate as its impact on epigenetic mechanisms will result in much more certain
and also efficacious healing techniques for the prevention and therapy of various diseases that
range from genetic conditions to other body disorders.
Conclusion::
With this assessment, we compile the existing information on the attributes of butyrate,
particularly its potential effects and also mechanisms involved in cancer, inflammation, diabetes
mellitus, neurological and cardiovascular disorder.
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Affiliation(s)
- Dhirendra Singh
- Department of Pharmacology, M.M. College of Pharmacy, (Deemed to be University), Mullana, Ambala, Haryana, India
| | - Sumeet Gupta
- Department of Pharmacology, M.M. College of Pharmacy, (Deemed to be University), Mullana, Ambala, Haryana, India
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112
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d'Enfert C, Kaune AK, Alaban LR, Chakraborty S, Cole N, Delavy M, Kosmala D, Marsaux B, Fróis-Martins R, Morelli M, Rosati D, Valentine M, Xie Z, Emritloll Y, Warn PA, Bequet F, Bougnoux ME, Bornes S, Gresnigt MS, Hube B, Jacobsen ID, Legrand M, Leibundgut-Landmann S, Manichanh C, Munro CA, Netea MG, Queiroz K, Roget K, Thomas V, Thoral C, Van den Abbeele P, Walker AW, Brown AJP. The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives. FEMS Microbiol Rev 2021; 45:fuaa060. [PMID: 33232448 PMCID: PMC8100220 DOI: 10.1093/femsre/fuaa060] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.
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Affiliation(s)
- Christophe d'Enfert
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Ann-Kristin Kaune
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Leovigildo-Rey Alaban
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Sayoni Chakraborty
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Neugasse 25, 07743 Jena, Germany
| | - Nathaniel Cole
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Margot Delavy
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Daria Kosmala
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Benoît Marsaux
- ProDigest BV, Technologiepark 94, B-9052 Gent, Belgium
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links, 9000 Ghent, Belgium
| | - Ricardo Fróis-Martins
- Immunology Section, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Moran Morelli
- Mimetas, Biopartner Building 2, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Diletta Rosati
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Marisa Valentine
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Zixuan Xie
- Gut Microbiome Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119–129, 08035 Barcelona, Spain
| | - Yoan Emritloll
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Peter A Warn
- Magic Bullet Consulting, Biddlecombe House, Ugbrook, Chudleigh Devon, TQ130AD, UK
| | - Frédéric Bequet
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
| | - Marie-Elisabeth Bougnoux
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Stephanie Bornes
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF0545, 20 Côte de Reyne, 15000 Aurillac, France
| | - Mark S Gresnigt
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Bernhard Hube
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Ilse D Jacobsen
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Mélanie Legrand
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Salomé Leibundgut-Landmann
- Immunology Section, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Chaysavanh Manichanh
- Gut Microbiome Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119–129, 08035 Barcelona, Spain
| | - Carol A Munro
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Karla Queiroz
- Mimetas, Biopartner Building 2, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Karine Roget
- NEXBIOME Therapeutics, 22 allée Alan Turing, 63000 Clermont-Ferrand, France
| | - Vincent Thomas
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
| | - Claudia Thoral
- NEXBIOME Therapeutics, 22 allée Alan Turing, 63000 Clermont-Ferrand, France
| | | | - Alan W Walker
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Alistair J P Brown
- MRC Centre for Medical Mycology, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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Ben Khedher M, Lo C, Diop K, Morand A, Armstrong N, Raoult D, Fenollar F. Taxonogenomics description of Arcanobacterium urinimassiliense sp. nov., a new bacterial species isolated from urine sample. New Microbes New Infect 2021; 41:100854. [PMID: 33854785 PMCID: PMC8027287 DOI: 10.1016/j.nmni.2021.100854] [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: 12/23/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/22/2022] Open
Abstract
Strain Marseille-P3248т is a new species from the order Actinomycetales that was isolated from the urine sample of a girl aged 20 months with rotavirus gastroenteritis. It is a facultative anaerobic Gram-positive rod-shaped bacterium. Strain Marseille-P3248т exhibits 94.73% sequence similarity with Arcanobacterium pluranimalium strain M430/94/2, a phylogenetically related species with standing in nomenclature. Its genome size is 1 667 964 bp with 49.1% G + C content. Strain Marseille-P3248т (= CSURP3248) is the type strain of the new species Arcanobacterium urinimassiliense sp. nov.
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Affiliation(s)
- M. Ben Khedher
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - K. Diop
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A. Morand
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - N. Armstrong
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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114
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Wongkuna S, Ghimire S, Chankhamhaengdecha S, Janvilisri T, Scaria J. Mediterraneibacter catenae SW178 sp. nov., an intestinal bacterium of feral chicken. PeerJ 2021; 9:e11050. [PMID: 33986975 PMCID: PMC8086573 DOI: 10.7717/peerj.11050] [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: 10/16/2020] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
A Gram-positive, coccobacillus, white raised and circular with an entire edge colony, and obligately anaerobic bacterium, strain SW178 was isolated from the cecum content of feral chickens in Brookings, South Dakota, USA. The most closely related strain based on 16S rRNA gene sequence analysis of strain SW178 was Mediterraneibacter torques ATCC 27756T (Ruminococcus torques ATCC 27756T) with 96.94% similarity. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. The optimal temperature and pH for growth in modified brain heart infusion (BHI-M) medium were 45 °C and pH 7.5, respectively. The sole carbon sources of the strain were dextrin, L-fucose, D-galacturonic, α-D-glucose, L-rhamnose and D-sorbitol. The primary cellular fatty acids were C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal (DMA). Based on the genotypic and phenotypic comparison, we proposed that strain SW178 belong to the genus Mediterraneibacter in the family Lachnospiraceae as a novel species, in which the name Mediterraneibacter catenae is proposed. The type strain is SW178 (= DSM 109242T = CCOS 1886T).
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Affiliation(s)
- Supapit Wongkuna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States
| | - Sudeep Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, United States
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, United States
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115
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Han P, Gu JQ, Li LS, Wang XY, Wang HT, Wang Y, Chang C, Sun JL. The Association Between Intestinal Bacteria and Allergic Diseases-Cause or Consequence? Front Cell Infect Microbiol 2021; 11:650893. [PMID: 33937097 PMCID: PMC8083053 DOI: 10.3389/fcimb.2021.650893] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022] Open
Abstract
The incidence of allergic disorders has been increasing over the past few decades, especially in industrialized countries. Allergies can affect people of any age. The pathogenesis of allergic diseases is complex and involves genetic, epigenetic, and environmental factors, and the response to medication is very variable. For some patients, avoidance is the sole effective therapy, and only when the triggers are identifiable. In recent years, the intestinal microbiota has emerged as a significant contributor to the development of allergic diseases. However, the precise mechanisms related to the effects of the microbiome on the pathogenesis of allergic diseases are unknown. This review summarizes the recent association between allergic disorders and intestinal bacterial dysbiosis, describes the function of gut microbes in allergic disease development from both preclinical and clinical studies, discusses the factors that influence gut microbial diversity and advanced techniques used in microbial analysis. Ultimately, more studies are required to define the host-microbial relationship relevant to allergic disorders and amenable to new therapeutic interventions.
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Affiliation(s)
- Pei Han
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Jian-Qing Gu
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Sha Li
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xue-Yan Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hong-Tian Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Christopher Chang
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
- Division of Pediatric Immunology and Allergy, Joe DiMaggio Children’s Hospital, Hollywood, FL, United States
| | - Jin-Lyu Sun
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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116
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Saraiva JP, Worrich A, Karakoç C, Kallies R, Chatzinotas A, Centler F, Nunes da Rocha U. Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021; 9:microorganisms9040840. [PMID: 33920040 PMCID: PMC8070991 DOI: 10.3390/microorganisms9040840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
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Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- Correspondence:
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117
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Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine. Appl Environ Microbiol 2021; 87:AEM.00088-21. [PMID: 33608289 DOI: 10.1128/aem.00088-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/08/2021] [Indexed: 12/22/2022] Open
Abstract
The isolation of bacteria that represent the diversity of autochthonous taxa in the gastrointestinal tract is necessary to fully ascertain their function, but the majority of bacterial species inhabiting the intestines of mammals are fastidious and thus challenging to isolate. The goal of the current study was to isolate a diverse assemblage of anaerobic bacteria from the intestine of pigs as a model animal and to comparatively examine various novel and traditional isolation strategies. Methods used included long-term enrichments, direct plating, a modified ichip method, as well as ethanol and tyndallization treatments of samples to select for endospore-forming taxa. A total of 234 taxa (91 previously uncultured) comprising 80 genera and 7 phyla were isolated from mucosal and luminal samples from the ileum, cecum, ascending colon, and spiral colon removed from animals under anesthesia. The diversity of bacteria isolated from the large intestine was less than that detected by next-generation sequence analysis. Long-term enrichments yielded the greatest diversity of recovered bacteria (Shannon's index [SI] = 4.7). Methods designed to isolate endospore-forming bacteria produced the lowest diversity (SI ≤ 2.7), with tyndallization yielding lower diversity than the ethanol method. However, the isolation frequency of previously uncultured bacteria was highest for ethanol-treated samples (41.9%) and the ichip method (32.5%). The goal of recovering a diverse collection of enteric bacteria was achieved. Importantly, the study findings demonstrate that it is necessary to use a combination of methods in concert to isolate bacteria that are representative of the diversity within the intestines of mammals.IMPORTANCE This work determined that using a combination of anaerobic isolation methods is necessary to increase the diversity of bacteria recovered from the intestines of monogastric mammals. Direct plating methods have traditionally been used to isolate enteric bacteria, and recent methods (e.g., diffusion methods [i.e., ichip] or differential isolation of endospore-forming bacteria) have been suggested to be superior at increasing diversity, including the recovery of previously uncultured taxa. We showed that long-term enrichment of samples using a variety of media isolated the most diverse and novel bacteria. Application of the ichip method delivered a diversity of bacteria similar to those of enrichment and direct plating methods. Methods that selected for endospore-forming bacteria generated collections that differed in composition from those of other methods with reduced diversity. However, the ethanol treatment frequently isolated novel bacteria. By using a combination of methods in concert, a diverse collection of enteric bacteria was generated for ancillary experimentation.
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118
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Pedobacter ghigonii sp. nov., Isolated from the Microbiota of the Planarian Schmidtea mediterranea. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12020019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The planarian S. mediterranea is a platyhelminth with worldwide distribution that can regenerate any part of its body after amputation and has the capacity to eliminate a large spectrum of human bacterial pathogens. Surprisingly, the microbiota of S. mediterranea remains poorly investigated. Using the culturomics strategy to study the bacterial component of planarians, we isolated a new bacterial strain, Marseille-Q2390, which we characterized with the taxono-genomic approach that associates phenotypic assays and genome sequencing and analysis. Strain Marseille-Q2390 exhibited a 16S rRNA sequence similarity of 99.36% with Pedobacter kyungheensis strain THG-T17T, the closest phylogenetic neighbor. It is a white-pigmented, Gram-negative, and rod-shaped bacterium. It grows in aerobic conditions and belongs to the family Sphingobacteriaceae. The genome of strain Marseille-Q2390 is 5,919,359 bp-long, with a G + C content of 40.3%. By comparing its genome with other closely related strains, the highest Orthologous Average Nucleotide Identity (Ortho-ANI) and digital DNA-DNA hybridization (dDDH) values were 85.71% and 30.50%, respectively, which were found with Pedobacter soli strain 15-51T. We conclude that strain Marseille-Q2390T is sufficiently different from other nearby species to be classified within a new species for which we propose the name Pedobacter ghigonii sp. nov.
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119
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Bordigoni A, Bouchard S, Desnues C. Isolation and Characterization of Gardnerella Phage vB_Gva_AB1, a Bacteriophage Infecting a Clinical Strain of Gardnerella vaginalis. Microbiol Resour Announc 2021; 10:e00053-21. [PMID: 33766896 PMCID: PMC7996455 DOI: 10.1128/mra.00053-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/24/2021] [Indexed: 11/20/2022] Open
Abstract
Gardnerella vaginalis is the presumed causative agent of bacterial vaginosis. Here, we describe the complete genome sequence of Gardnerella phage vB_Gva_AB1, induced from a vaginal bacterial strain from a woman suffering with bacterial vaginosis. The phage double-stranded DNA (dsDNA) genome is 50,268 bp long with a GC content of 39.55% and contains 62 predicted open reading frames.
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Affiliation(s)
- Alexia Bordigoni
- Aix-Marseille Université, IRD 198, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Marseille, France
| | - Sonia Bouchard
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography, UM 110, Marseille, France
| | - Christelle Desnues
- Aix-Marseille Université, IRD 198, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography, UM 110, Marseille, France
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120
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Penland M, Falentin H, Parayre S, Pawtowski A, Maillard MB, Thierry A, Mounier J, Coton M, Deutsch SM. Linking Pélardon artisanal goat cheese microbial communities to aroma compounds during cheese-making and ripening. Int J Food Microbiol 2021; 345:109130. [PMID: 33735781 DOI: 10.1016/j.ijfoodmicro.2021.109130] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 11/17/2022]
Abstract
Pélardon is an artisanal French raw goat's milk cheese, produced using natural whey as a backslop. The aim of this study was to identify key microbial players involved in the acidification and aroma production of this Protected Designation of Origin cheese. Microbial diversity of samples, collected from the raw milk to 3-month cheese ripening, was determined by culture-dependent (MALDI-TOF analysis of 2877 isolates) and -independent (ITS2 and 16S metabarcoding) approaches and linked to changes in biochemical profiles (volatile compounds and acids). In parallel, potential dominant autochthonous microorganism reservoirs were also investigated by sampling the cheese-factory environment. Complex and increasing microbial diversity was observed by both approaches during ripening although major discrepancies were observed regarding Lactococcus lactis and Lacticaseibacillus paracasei fate. By correlating microbial shifts to biochemical changes, Lactococcus lactis was identified as the main acidifying bacterium, while L. mesenteroides and Geotrichum candidum were prevalent and associated with amino acids catabolism after the acidification step. The three species were dominant in the whey (backslop). In contrast, L. paracasei, Enterococcus faecalis, Penicillium commune and Scopulariopsis brevicaulis, which dominated during ripening, likely originated from the cheese-making environment. All these four species were positively correlated to major volatile compounds responsible for the goaty and earthy Pélardon cheese aroma. Overall, this work highlighted the power of MALDI-TOF and molecular techniques combined with volatilome analyses to dynamically follow and identify microbial communities during cheese-making and successively identify the key-players involved in aroma production and contributing to the typicity of Pélardon cheese.
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Affiliation(s)
- Marine Penland
- STLO, INRAE, Institut Agro, 35042 Rennes, France; Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | | | | | - Audrey Pawtowski
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | | | - Anne Thierry
- STLO, INRAE, Institut Agro, 35042 Rennes, France
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
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121
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Naud S, Bellali S, Anani H, Lo C, Yacouba A, Tidjani Alou M, Armstrong N, Bonvalet M, Zitvogel L, Raoult D, Lagier JC. Luxibacter massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota. New Microbes New Infect 2021; 40:100850. [PMID: 33732473 PMCID: PMC7941043 DOI: 10.1016/j.nmni.2021.100850] [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: 12/11/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/22/2022] Open
Abstract
An anaerobic facultative Gram-stain positive bacterium was isolated from human gut microbiota. Strain Marseille-P5551T was considered to be a new genus within the phylum Firmicutes, as it exhibits a 91.87% similarity level with Faecalicatena orotica (NR_117129.1), the phylogenetically closest related species. The draft genome size of strain Marseille-P5551T is 4 142 938 bp with 44.4% of G + C content. We hereby suggest the creation of Luxibacter massiliensis gen. nov., sp. nov., as a new bacterial genus.
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Affiliation(s)
- S. Naud
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - S. Bellali
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - H. Anani
- IHU-Méditerranée Infection, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A. Yacouba
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - M. Tidjani Alou
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - N. Armstrong
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - M. Bonvalet
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - L. Zitvogel
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - D. Raoult
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
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122
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Mitter EK, Tosi M, Obregón D, Dunfield KE, Germida JJ. Rethinking Crop Nutrition in Times of Modern Microbiology: Innovative Biofertilizer Technologies. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.606815] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Global population growth poses a threat to food security in an era of increased ecosystem degradation, climate change, soil erosion, and biodiversity loss. In this context, harnessing naturally-occurring processes such as those provided by soil and plant-associated microorganisms presents a promising strategy to reduce dependency on agrochemicals. Biofertilizers are living microbes that enhance plant nutrition by either by mobilizing or increasing nutrient availability in soils. Various microbial taxa including beneficial bacteria and fungi are currently used as biofertilizers, as they successfully colonize the rhizosphere, rhizoplane or root interior. Despite their great potential to improve soil fertility, biofertilizers have yet to replace conventional chemical fertilizers in commercial agriculture. In the last 10 years, multi-omics studies have made a significant step forward in understanding the drivers, roles, processes, and mechanisms in the plant microbiome. However, translating this knowledge on microbiome functions in order to capitalize on plant nutrition in agroecosystems still remains a challenge. Here, we address the key factors limiting successful field applications of biofertilizers and suggest potential solutions based on emerging strategies for product development. Finally, we discuss the importance of biosafety guidelines and propose new avenues of research for biofertilizer development.
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123
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Park H, Yeo S, Kang S, Huh CS. Longitudinal Microbiome Analysis in a Dextran Sulfate Sodium-Induced Colitis Mouse Model. Microorganisms 2021; 9:370. [PMID: 33673349 PMCID: PMC7917662 DOI: 10.3390/microorganisms9020370] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
The role of the gut microbiota in the pathogenesis of inflammatory bowel disease (IBD) has been in focus for decades. Although metagenomic observations in patients/animal colitis models have been attempted, the microbiome results were still indefinite and broad taxonomic presumptions were made due to the cross-sectional studies. Herein, we conducted a longitudinal microbiome analysis in a dextran sulfate sodium (DSS)-induced colitis mouse model with a two-factor design based on serial DSS dose (0, 1, 2, and 3%) and duration for 12 days, and four mice from each group were sacrificed at two-day intervals. During the colitis development, a transition of the cecal microbial diversity from the normal state to dysbiosis and dynamic changes of the populations were observed. We identified genera that significantly induced or depleted depending on DSS exposure, and confirmed the correlations of the individual taxa to the colitis severity indicated by inflammatory biomarkers (intestinal bleeding and neutrophil-derived indicators). Of note, each taxonomic population showed its own susceptibility to the changing colitis status. Our findings suggest that an understanding of the individual susceptibility to colitis conditions may contribute to identifying the role of the gut microbes in the pathogenesis of IBD.
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Affiliation(s)
- Hyunjoon Park
- Research Institute of Eco-Friendly Livestock Science, Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea;
- Advanced Green Energy and Environment Institute, Handong Global University, Pohang 37554, Korea
| | - Soyoung Yeo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea;
| | - Seokwon Kang
- Department of Life Sciences, Handong Global University, Pohang 37554, Korea;
| | - Chul Sung Huh
- Research Institute of Eco-Friendly Livestock Science, Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea;
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea
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124
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Negativibacillus massiliensis gen. nov., sp. nov., a New Bacterial Genus Isolated from a Human Left Colon Sample. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12010004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A new genus, a member of the Ruminococcaceae family, was isolated from the left colon of a healthy woman. Strain Marseille P3213 was a non-motile, spore-forming, Gram-stain negative, rod-shaped bacterium. This strictly anaerobic species reached optimal growth after an incubation of 72 h at 37 °C. The 16S rRNA gene sequence of this strain shared a 93.52% similarity level with Harryflintia acetispora strain V20-281a, its closest phylogenetic neighbor with standing in the nomenclature. Its genome had a size of 2.87 Mb, with a 45.81% G + C content. We hereby propose the creation of Negativibacillus massiliensis strain P3213T as the 43rd genus within the Ruminococcaceae family.
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125
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Thrash JC. Towards culturing the microbe of your choice. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:36-41. [PMID: 33073476 DOI: 10.1111/1758-2229.12898] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Affiliation(s)
- J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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126
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Morand A, Tall ML, Kuete Yimagou E, Ngom II, Lo CI, Cornu F, Tsimaratos M, Lagier JC, Levasseur A, Raoult D, Fournier PE. Anaerococcus urinimassiliensis sp. nov., a new bacterium isolated from human urine. Sci Rep 2021; 11:2684. [PMID: 33514860 PMCID: PMC7846727 DOI: 10.1038/s41598-021-82420-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 10/20/2020] [Indexed: 12/22/2022] Open
Abstract
To date there are thirteen species validly assigned to the genus Anaerococcus. Most of the species in this genus are anaerobic and of human origin. Anaerococcus urinimassiliensis sp. nov., strain Marseille-P2143T is member of family Peptoniphilaceae, which was isolated from the urine of a 17-year-old boy affected by autoimmune hepatitis and membranoproliferative glomerulonephritis using the culturomic approach. In the current study, a taxono-genomics method was employed to describe this new species. The strain Marseille-P2143T was gram positive cocci with translucent colonies on blood agar. Its genome was 2,189,509 bp long with a 33.5 mol% G + C content and exhibited 98.48% 16S rRNA similarity with Anaerococcus provencensis strain 9,402,080. When Anaerococcus urinomassiliensis strain Marseill-P2143T is compared with closely related species, the values ranged from 71.23% with A. hydrogenalis strain DSM 7454T (NZ_ABXA01000052.1) to 90.64% with A. provencensis strain 9402080T (NZ_HG003688.1). This strain has implemented the repertoire of known bacteria of the human urinary tract.
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Affiliation(s)
- Aurélie Morand
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,Pédiatrie Spécialisée Et Médecine Infantile, Hôpital de La Timone, AP-HM, Marseille, France.
| | - Mamadou Lamine Tall
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Edmond Kuete Yimagou
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Issa Isaac Ngom
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Cheikh Ibrahima Lo
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Florent Cornu
- Pédiatrie Multidisciplinaire, Hôpital de La Timone, AP-HM, Marseille, France
| | - Michel Tsimaratos
- Pédiatrie Multidisciplinaire, Hôpital de La Timone, AP-HM, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Institut Universitaire de France (IUF), Paris, France
| | - Didier Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
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127
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Zotta T, Ricciardi A, Condelli N, Parente E. Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture. Crit Rev Food Sci Nutr 2021; 62:3898-3912. [PMID: 33455430 DOI: 10.1080/10408398.2020.1870927] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Undefined strain starters are used for the production of many traditional and artisanal cheeses. Composition of undefined starters depends on several factors, and the diversity in strains and species significantly affects cheese quality and features. Culture-dependent approaches have long been used for the microbial profiling and functionalities of undefined cultures but underestimate their diversity due to culturability biases. Recently, culture-independent methods, based on high-throughput sequencing (HTS), have been preferred, with a significant boost in resolution power and sensitivity level. Amplicon targeted (AT) metagenomics, based on 16S rRNA sequencing, returned a larger microbiota diversity at genus and, sometimes, at species levels for artisanal starters of several PDO cheeses, but was inappropriate for populations with high strain diversity, and other gene targets were tested in AT approaches. Shotgun metagenomics (total DNA) and metatranscriptomics (total RNA), although are more powerful in depicting diversity and functionality of undefined cultures, have been rarely applied because of some limitations (e.g., high costs and laboriousness, need for bioinformatics skills). The advantages of HTS technologies are undoubted, but some hurdles need to be still overcame (e.g., resolution power, discrepancy between active and inactive cells, robust analytic pipelines, cost and time reduction for integrated approaches) so that HTS become routinary and convenient for defining complexity, microbial interactions (including host-phage relationships) and evolution in cheeses of undefined starters.
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Affiliation(s)
- Teresa Zotta
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Annamaria Ricciardi
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Nicola Condelli
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Eugenio Parente
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
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128
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Huang X, Li P, Zhou M, Li Y, Ou X, Chen P, Guggenberger G, Liu BF. A high-throughput ultrasonic spraying inoculation method promotes colony cultivation of rare microbial species. Environ Microbiol 2021; 23:1275-1285. [PMID: 33400374 DOI: 10.1111/1462-2920.15386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/28/2020] [Accepted: 01/03/2021] [Indexed: 11/30/2022]
Abstract
Current method for obtaining microbial colonies still relies on traditional dilution and spreading plate (DSP) procedures, which is labor-intensive, skill-dependent, low-throughput and inevitably causing dilution-to-extinction of rare microorganisms. Herein, we proposed a novel ultrasonic spraying inoculation (USI) method that disperses microbial suspensions into millions of aerosols containing single cells, which lately be deposited freely on a gel plate to achieve high-throughput culturing of colonies. Compared with DSP, USI significantly increased both distributing uniformity and throughput of the colonies on agar plates, improving the minimal colony-forming abundance of rare Escherichia coli mixed in a lake sample from 1% to 0.01%. Applying this novel USI to a lake sample, 16 cellulose-degrading colonies were screened out among 4766 colonies on an enlarged 150-mm-diameter LB plate. Meanwhile, they could only be occasionally observed when using commonly used DSP procedures. 16S rRNA sequencing further showed that USI increased colony-forming species from 11 (by DSP) to 23, including seven completely undetectable microorganisms in DSP-reared communities. In addition to avoidance of dilution-to-extinction, operation-friendly USI efficiently inoculated microbial samples on the agar plate in a high-throughput and single-cell form, which eliminated masking or out-competition from other species in associated groups, thereby improving rare species cultivability.
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Affiliation(s)
- Xizhi Huang
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pengjie Li
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mengfan Zhou
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yiwei Li
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaowen Ou
- Hubei Key Laboratory of Purification and Application of Plant Anti-Cancer Active Ingredients, Department of Chemistry and Life Science, Hubei University of Education, No. 129, Gaoxin 2nd Road, East Lake High-Tech Zone, Wuhan, 430205, China
| | - Peng Chen
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Georg Guggenberger
- Institute of Soil Science, Leibniz University Hannover, Hannover, 30419, Germany
| | - Bi-Feng Liu
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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129
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Moossavi S, Fontes ME, Rossi L, Fusch G, Surette MG, Azad MB. Capturing the diversity of the human milk microbiota through culture-enriched molecular profiling: a feasibility study. FEMS Microbiol Lett 2021; 368:6070652. [PMID: 33417698 DOI: 10.1093/femsle/fnab001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Previous human milk studies have confirmed the existence of a highly diverse bacterial community using culture-independent and targeted culture-dependent techniques. However, culture-enriched molecular profiling of milk microbiota has not been done. Additionally, the impact of storage conditions and milk fractionation on microbiota composition is not understood. In this feasibility study, we optimized and applied culture-enriched molecular profiling to study culturable milk microbiota in eight milk samples collected from mothers of infants admitted to a neonatal intensive care unit. Fresh samples were immediately plated or stored at -80°C for 2 weeks (short-term frozen). Long-term samples were stored at -20°C for >6 months. Samples were cultured using 10 different culture media and incubated both aerobically and anaerobically. We successfully isolated major milk bacteria, including Streptococcus, Staphylococcus and Bifidobacterium, from fresh milk samples, but were unable to culture any bacteria from the long-term frozen samples. Short-term freezing shifted the composition of viable milk bacteria from the original composition in fresh samples. Nevertheless, the inter-individual variability of milk microbiota composition was observed even after short-term storage. There was no major difference in the overall milk microbiota composition between milk fractions in this feasibility study. This is among the first studies on culture-enriched molecular profiling of the milk microbiota demonstrating the effect of storage and fractionation on milk microbiota composition.
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Affiliation(s)
- Shirin Moossavi
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.,Manitoba Interdisciplinary Lactation Centre (MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada.,Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 14117-13135, Iran.,Microbiome and Microbial Ecology Interest Group (MMEIG), Universal Scientific Education and Research Network (USERN), Calgary, AB T2N 4Z1, Canada
| | - Michelle E Fontes
- Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Laura Rossi
- Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Gerhard Fusch
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Michael G Surette
- Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Meghan B Azad
- Manitoba Interdisciplinary Lactation Centre (MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada.,Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
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130
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Noone JC, Helmersen K, Leegaard TM, Skråmm I, Aamot HV. Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies. Microorganisms 2021; 9:microorganisms9010097. [PMID: 33406597 PMCID: PMC7823515 DOI: 10.3390/microorganisms9010097] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/26/2022] Open
Abstract
Conventional culture-based diagnostics of orthopaedic-implant-associated infections (OIAIs) are arduous. Hence, the aim of this study was to evaluate a culture-independent, rapid nanopore-based diagnostic protocol with regard to (a) pathogen identification, (b) time to pathogen identification, and (c) identification of antimicrobial resistance (AMR). This prospective proof-of-concept study included soft tissue biopsies from 32 patients with OIAIs undergoing first revision surgery at Akershus University Hospital, Norway. The biopsies were divided into two segments. Nanopore shotgun metagenomic sequencing and pathogen and antimicrobial resistance gene identification using the EPI2ME analysis platform (Oxford Nanopore Technologies) were performed on one segment. Conventional culture-based diagnostics were performed on the other. Microbial identification matched in 23/32 OIAI patients (72%). Sequencing detected additional microbes in 9/32 patients. Pathogens detected by culturing were identified by sequencing within a median of 1 h of sequencing start [range 1–18 h]. Phenotypic AMR was explained by the detection of resistance genes in 11/23 patients (48%). Diagnostics of OIAIs using shotgun metagenomics sequencing are possible within 24 h from biopsy using nanopore technology. Sequencing outperformed culturing with respect to speed and pathogen detection where pathogens were at sufficient concentration, whereas culture-based methods had an advantage at lower pathogen concentrations. Sequencing-based AMR detection may not yet be a suitable replacement for culture-based antibiotic susceptibility testing.
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Affiliation(s)
- J. Christopher Noone
- Department of Microbiology and Infection Control, Akershus University Hospital, 1478 Lørenskog, Norway; (K.H.); (T.M.L.); (H.V.A.)
- Faculty of Medicine, University of Oslo, 0316 Oslo, Norway
- Correspondence: ; Tel.: +47-924-80-857
| | - Karin Helmersen
- Department of Microbiology and Infection Control, Akershus University Hospital, 1478 Lørenskog, Norway; (K.H.); (T.M.L.); (H.V.A.)
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital and University of Oslo, 1478 Lørenskog, Norway
| | - Truls Michael Leegaard
- Department of Microbiology and Infection Control, Akershus University Hospital, 1478 Lørenskog, Norway; (K.H.); (T.M.L.); (H.V.A.)
- Faculty of Medicine, University of Oslo, 0316 Oslo, Norway
| | - Inge Skråmm
- Orthopaedic Clinic, Akershus University Hospital, 1478 Lørenskog, Norway;
| | - Hege Vangstein Aamot
- Department of Microbiology and Infection Control, Akershus University Hospital, 1478 Lørenskog, Norway; (K.H.); (T.M.L.); (H.V.A.)
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131
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Matson V, Chervin CS, Gajewski TF. Cancer and the Microbiome-Influence of the Commensal Microbiota on Cancer, Immune Responses, and Immunotherapy. Gastroenterology 2021; 160:600-613. [PMID: 33253684 PMCID: PMC8409239 DOI: 10.1053/j.gastro.2020.11.041] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023]
Abstract
The commensal microbiota has been implicated in the regulation of a diverse array of physiological processes, both within the gastrointestinal tract and at distant tissue sites. Cancer is no exception, and distinct aspects of the microbiota have been reported to have either pro- or anti-tumor effects. The functional role of the microbiota in regulating not only mucosal but also systemic immune responses has led to investigations into the impact on cancer immunotherapies, particularly with agents targeting the immunologic checkpoints PD-1 and CTLA-4. Microbial sequencing and reconstitution of germ-free mice have indicated both positive and negative regulatory bacteria likely exist, which either promote or interfere with immunotherapy efficacy. These collective findings have led to the development of clinical trials pursuing microbiome-based therapeutic interventions, with the hope of expanding immunotherapy efficacy. This review summarizes recent knowledge about the relationship between the host microbiota and cancer and anti-tumor immune response, with implications for cancer therapy.
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132
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Zhao Y, Yu L, Tian F, Zhao J, Zhang H, Chen W, Zhai Q. An optimized culture medium to isolate Lactobacillus fermentum strains from the human intestinal tract. Food Funct 2021; 12:6740-6754. [PMID: 34105590 DOI: 10.1039/d1fo00209k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Research studies have shown that Lactobacillus fermentum generally exists in the human gut and has potential health benefits on host health due to its antimicrobial and antioxidant properties. However, the lack of an effective culture medium for the isolation of L. fermentum has presented a significant obstacle on the path to screen L. fermentum strains from the human intestinal tract with a large diversity of commensal microbes. In this study, a total of 51 Lactobacillus species are detected in 200 human fecal samples and we aim to distinguish L. fermentum from these common existing Lactobacillus species and design a more efficient culture medium for isolating L. fermentum strains from the human gut. Based on antibiotic susceptibility and sugar utilization tests, a new optimized medium called LFMATA containing arabinose as the carbon source and 20 mg L-1 vancomycin, 64 mg L-1 gentamicin and 256 mg L-1 streptomycin was developed. Genotype and phenotype analysis for antibiotic resistance and carbohydrate metabolism showed that though glycometabolism-related genes (araA, xylA, manX, bglX, treP and rbsK) correlated with the carbon utilization of Lactobacillus, the genes conferring resistance to streptomycin (gidB and rpsL) and gentamicin (tlyA) were not directly associated with the antibiotic resistance of Lactobacillus strains. This new selective medium greatly increased the efficiency of screening L. fermentum strains from human fecal samples, with the rate of L. fermentum isolation on LFMATA being 10-fold higher than that on LAMVAB.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R China.
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133
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Egan M, Dempsey E, Ryan CA, Ross RP, Stanton C. The Sporobiota of the Human Gut. Gut Microbes 2021; 13:1-17. [PMID: 33406976 PMCID: PMC7801112 DOI: 10.1080/19490976.2020.1863134] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 02/04/2023] Open
Abstract
The human gut microbiome is a diverse and complex ecosystem that plays a critical role in health and disease. The composition of the gut microbiome has been well studied across all stages of life. In recent years, studies have investigated the production of endospores by specific members of the gut microbiome. An endospore is a tough, dormant structure formed by members of the Firmicutes phylum, which allows for greater resistance to otherwise inhospitable conditions. This innate resistance has consequences for human health and disease, as well as in biotechnology. In particular, the formation of endospores is strongly linked to antibiotic resistance and the spread of antibiotic resistance genes, also known as the resistome. The term sporobiota has been used to define the spore-forming cohort of a microbial community. In this review, we present an overview of the current knowledge of the sporobiota in the human gut. We discuss the development of the sporobiota in the infant gut and the perinatal factors that may have an effect on vertical transmission from mother to infant. Finally, we examine the sporobiota of critically important food sources for the developing infant, breast milk and powdered infant formula.
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Affiliation(s)
- Muireann Egan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eugene Dempsey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - C. Anthony Ryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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134
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Shanahan F, Ghosh TS, O'Toole PW. The Healthy Microbiome-What Is the Definition of a Healthy Gut Microbiome? Gastroenterology 2021; 160:483-494. [PMID: 33253682 DOI: 10.1053/j.gastro.2020.09.057] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/19/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023]
Abstract
Use of microbiome-based biomarkers in diagnosis, prognosis, risk profiling, and precision therapy requires definition of a healthy microbiome in different populations. To determine features of the intestinal microbiota associated with health, however, we need improved microbiome profiling technologies, with strain-level resolution. We must also learn more about how the microbiome varies among apparently healthy people, how it changes with age, and the effects of diet, medications, ethnicity, geography, and lifestyle. Furthermore, many intestinal microbes, including viruses, phage, fungi, and archaea, have not been characterized, and little is known about their contributions to health and disease.Whether a healthy microbiome can be defined is an important and seemingly simple question, but with a complex answer in continual need of refinement.
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Affiliation(s)
- Fergus Shanahan
- Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland; APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland.
| | - Tarini S Ghosh
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland; School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland; School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
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135
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Updating the repertoire of cultured bacteria from the human being. Microb Pathog 2020; 150:104698. [PMID: 33347961 DOI: 10.1016/j.micpath.2020.104698] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 12/19/2022]
Abstract
The recent renewal of cultural approach has substantially enriched knowledge of the human microbiota, notably through the discovery of new taxa from various anatomical sites. As an increasing number of these recent species are currently considered beneficial or harmful for human health, a constant updating of the repertoire of bacteria and archaea isolated from humans by culture is essential. Herein, we show that the number of cultured bacterial species associated with human beings increased, from 2776 in 2018, to 3253 in 2020, representing a 17% increase in 2 years by adding 477 species, of which 64% are new species (N = 307). A wide majority of the species added (i.e., 63%) were isolated using the culturomics approach, while 16% were cultured as part of clinical microbiology laboratories. Human microbiota studies would benefit from the completeness of the repertoire of bacteria associated with human beings, which would require continued efforts to culture microbes from human specimens.
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136
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Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review. SUSTAINABILITY 2020. [DOI: 10.3390/su13010010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.
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137
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Naud S, Khelaifia S, Mbogning Fonkou MD, Dione N, Lagier JC, Raoult D. Proof of Concept of Culturomics Use of Time of Care. Front Cell Infect Microbiol 2020; 10:524769. [PMID: 33330116 PMCID: PMC7719802 DOI: 10.3389/fcimb.2020.524769] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/22/2020] [Indexed: 12/22/2022] Open
Abstract
Culturomics, a high throughput culture method with rapid identification of the colonies by Matrix Assisted Laser Desorption Ionization/Time Of Flight Mass Spectrometry (MALDI-TOF MS), has demonstrated its contribution to the exploration of the gut microbiota over the past 10 years. However, the cost, work time and workload, considerably limit its use on a large scale or emergency context. Here, by testing two different stool samples, including a stool sample from a patient requiring rapid immunotherapy treatment, we tested a new fast culturomic protocol using two pre-incubation media, blood culture bottle and YCFA modified medium. Both media were supplemented with 2 ml of rumen fluid filtered at 0.2 μm and 2 ml of defibrinated and sterile sheep blood. Unlike the standard culturomics, subculturing of blood culture bottle were performed at reduced incubation time (3 h, 6 h, 9 h, 24 h) and at a longer incubation time (3 days, 7 days, and 10 days) at 37°C. By testing 5,200 colonies per MALDI-TOF MS and obtaining a comparable number of cultured bacterial species (131 to 143) in a stool sample, this new protocol reduced the number of colonies tested by 57%, working time by 78.6% and cost by 72.2%. In addition, we highlighted that the proportion of strict anaerobic species has increased by 24%, known to be the preferential targets for biotherapy, including Faecalibacterium prausnitzii, Akkermansia muciniphila, Christensenella minuta, and Phascolarctobacterium faecium. Finally, this work showed that some bacterial species grew earlier but disappeared with prolonged incubation times.
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Affiliation(s)
- Sabrina Naud
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Saber Khelaifia
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Maxime Descartes Mbogning Fonkou
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Niokhor Dione
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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138
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Eukaryotic and Prokaryotic Microbiota Interactions. Microorganisms 2020; 8:microorganisms8122018. [PMID: 33348551 PMCID: PMC7767281 DOI: 10.3390/microorganisms8122018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 12/12/2022] Open
Abstract
The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies were analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.
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139
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Duong B, Marraccini P, Maeght JL, Vaast P, Lebrun M, Duponnois R. Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.607935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Intensive coffee production is accompanied by several environmental issues, including soil degradation, biodiversity loss, and pollution due to the wide use of agrochemical inputs and wastes generated by processing. In addition, climate change is expected to decrease the suitability of cultivated areas while potentially increasing the distribution and impact of pests and diseases. In this context, the coffee microbiota has been increasingly studied over the past decades in order to improve the sustainability of the coffee production. Therefore, coffee associated microorganisms have been isolated and characterized in order to highlight their useful characteristics and study their potential use as sustainable alternatives to agrochemical inputs. Indeed, several microorganisms (including bacteria and fungi) are able to display plant growth-promoting capacities and/or biocontrol abilities toward coffee pests and diseases. Despite that numerous studies emphasized the potential of coffee-associated microorganisms under controlled environments, the present review highlights the lack of confirmation of such beneficial effects under field conditions. Nowadays, next-generation sequencing technologies allow to study coffee associated microorganisms with a metabarcoding/metagenomic approach. This strategy, which does not require cultivating microorganisms, now provides a deeper insight in the coffee-associated microbial communities and their implication not only in the coffee plant fitness but also in the quality of the final product. The present review aims at (i) providing an extensive description of coffee microbiota diversity both at the farming and processing levels, (ii) identifying the “coffee core microbiota,” (iii) making an overview of microbiota ability to promote coffee plant growth and to control its pests and diseases, and (iv) highlighting the microbiota potential to improve coffee quality and waste management sustainability.
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140
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Bittar F, Gouriet F, Khelaifia S, Raoult D, Ranque S. FastFung: A novel medium for the culture and isolation of fastidious fungal species from clinical samples. J Microbiol Methods 2020; 180:106108. [PMID: 33232796 DOI: 10.1016/j.mimet.2020.106108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022]
Abstract
We developed a novel culture medium, referred to FastFung medium as suitable for the culture of clinical fungi, including fastidious ones, for both research and diagnostic studies. It is based on Schædler agar supplemented with many essential components for the growth of fastidious fungi. It also contains selective antibacterial agents for the inhibition of contaminant bacteria growth. In this preliminary study, the FastFung medium was compared to the gold standard Sabouraud medium for 98 fungal and 20 bacterial strains. The fungal strain positive culture rate was 100% vs. 95% and the bacterial strain inhibition was 100% vs. 20%, for the FastFung and Sabouraud media, respectively. When compared to the Sabouraud medium on 120 clinical samples, the FastFung medium displayed both a higher fungal colonies count, and a lower culture contamination rate. Storage at 4 °C for 4 weeks did not alter the FastFung culture medium performances for the six isolates of Candida, Cryptococcus, and Penicillium tested. These encouraging results suggest future development of using the FastFung medium in clinical mycology and in mycobiome characterization. Further prospective evaluation aiming at assessing whether implementing the FastFung medium in the routine workflow simplifies and strengthen fungal isolation capacities in the clinical laboratory is warranted.
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Affiliation(s)
- Fadi Bittar
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Frédérique Gouriet
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Saber Khelaifia
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Stéphane Ranque
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France; IHU Méditerranée Infection, Marseille, France.
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141
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Fernández L, Pannaraj PS, Rautava S, Rodríguez JM. The Microbiota of the Human Mammary Ecosystem. Front Cell Infect Microbiol 2020; 10:586667. [PMID: 33330129 PMCID: PMC7718026 DOI: 10.3389/fcimb.2020.586667] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Human milk contains a dynamic and complex site-specific microbiome, which is not assembled in an aleatory way, formed by organized microbial consortia and networks. Presence of some genera, such as Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium (formerly known as Propionibacterium), Lactobacillus, Lactococcus and Bifidobacterium, has been detected by both culture-dependent and culture-independent approaches. DNA from some gut-associated strict anaerobes has also been repeatedly found and some studies have revealed the presence of cells and/or nucleic acids from viruses, archaea, fungi and protozoa in human milk. Colostrum and milk microbes are transmitted to the infant and, therefore, they are among the first colonizers of the human gut. Still, the significance of human milk microbes in infant gut colonization remains an open question. Clinical studies trying to elucidate the question are confounded by the profound impact of non-microbial human milk components to intestinal microecology. Modifications in the microbiota of human milk may have biological consequences for infant colonization, metabolism, immune and neuroendocrine development, and for mammary health. However, the factors driving differences in the composition of the human milk microbiome remain poorly known. In addition to colostrum and milk, breast tissue in lactating and non-lactating women may also contain a microbiota, with implications in the pathogenesis of breast cancer and in some of the adverse outcomes associated with breast implants. This and other open issues, such as the origin of the human milk microbiome, and the current limitations and future prospects are addressed in this review.
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Affiliation(s)
- Leónides Fernández
- Department of Galenic Pharmacy and Food Technology, Complutense University of Madrid, Madrid, Spain
| | - Pia S. Pannaraj
- Department of Pediatrics and Molecular Microbiology and Immunology, Keck School of Medicine and Children’s Hospital, Los Angeles, CA, United States
| | - Samuli Rautava
- University of Helsinki and Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
| | - Juan M. Rodríguez
- Department of Nutrition and Food Science, Complutense University of Madrid, Madrid, Spain
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142
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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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Lo CI, Niang EHA, Sarr M, Durand G, Tall ML, Caputo A, Raoult D, Fournier PE, Fenollar F. Fenollaria timonensis sp. nov., A New Bacterium Isolated from Healthy Human Fresh Stool. Curr Microbiol 2020; 77:3780-3786. [PMID: 32920691 DOI: 10.1007/s00284-020-02151-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022]
Abstract
The strain Marseille-P2133 is the type strain of a new bacterial species of the order Clostridiales that was isolated from a stool sample from a healthy volunteer. It is a strictly anaerobic Gram-negative coccobacillus. MALDI-TOF MS did not provide any identification. Strain Marseille-P2133T exhibits 97.4% similarity levels with the Fenollaria massiliensis strain 9401234T (NR_133038), a phylogenetically related species with standing in nomenclature. On the basis of these data, we propose the creation of Fenollaria timonensis sp. nov.
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Affiliation(s)
- Cheikh Ibrahima Lo
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - El Hadj Amadou Niang
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
| | - Marièma Sarr
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
| | - Guillaume Durand
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
| | - Mamadou Lamine Tall
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
| | - Aurélia Caputo
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Florence Fenollar
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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144
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State of the Art in the Culture of the Human Microbiota: New Interests and Strategies. Clin Microbiol Rev 2020; 34:34/1/e00129-19. [PMID: 33115723 DOI: 10.1128/cmr.00129-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization-time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.
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145
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Dalal N, Jalandra R, Sharma M, Prakash H, Makharia GK, Solanki PR, Singh R, Kumar A. Omics technologies for improved diagnosis and treatment of colorectal cancer: Technical advancement and major perspectives. Biomed Pharmacother 2020; 131:110648. [PMID: 33152902 DOI: 10.1016/j.biopha.2020.110648] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/09/2020] [Accepted: 08/16/2020] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) ranks third among the most commonly occurring cancers worldwide, and it causes half a million deaths annually. Alongside mechanistic study for CRC detection and treatment by conventional techniques, new technologies have been developed to study CRC. These technologies include genomics, transcriptomics, proteomics, and metabolomics which elucidate DNA markers, RNA transcripts, protein and, metabolites produced inside the colon and rectum part of the gut. All these approaches form the omics arena, which presents a remarkable opportunity for the discovery of novel prognostic, diagnostic and therapeutic biomarkers and also delineate the underlying mechanism of CRC causation, which may further help in devising treatment strategies. This review also mentions the latest developments in metagenomics and culturomics as emerging evidence suggests that metagenomics of gut microbiota has profound implications in the causation, prognosis, and treatment of CRC. A majority of bacteria cannot be studied as they remain unculturable, so culturomics has also been strengthened to develop culture conditions suitable for the growth of unculturable bacteria and identify unknown bacteria. The overall purpose of this review is to succinctly evaluate the application of omics technologies in colorectal cancer research for improving the diagnosis and treatment strategies.
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Affiliation(s)
- Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India; Department of Environmental Science, Satyawati College, Delhi University, Delhi 110052, India
| | - Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India; Department of Zoology, Maharshi Dayanand University, Rohtak 124001, India
| | - Minakshi Sharma
- Department of Zoology, Maharshi Dayanand University, Rohtak 124001, India
| | - Hridayesh Prakash
- Amity Institute of Virology and Immunology, Amity University, Sector 125, Noida 201313, Uttar Pradesh, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pratima R Solanki
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajeev Singh
- Department of Environmental Science, Satyawati College, Delhi University, Delhi 110052, India.
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India.
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146
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Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country. Diagnostics (Basel) 2020; 10:diagnostics10100816. [PMID: 33066371 PMCID: PMC7602188 DOI: 10.3390/diagnostics10100816] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 10/11/2020] [Indexed: 12/19/2022] Open
Abstract
Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries.
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147
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Culturomics Discloses Anti-Tubercular Enterococci Exclusive of Pulmonary Tuberculosis: A Preliminary Report. Microorganisms 2020; 8:microorganisms8101544. [PMID: 33036349 PMCID: PMC7599504 DOI: 10.3390/microorganisms8101544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/25/2020] [Accepted: 10/04/2020] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium tuberculosis causes pulmonary tuberculosis, a deadly infection of which the clinical expression and prognosis are not fully understood at the individual level, apart from genetic susceptibility traits. We investigated whether individual gut microbiota may correlate with pulmonary tuberculosis status. Culturomics investigations of gut microbiota in two pulmonary tuberculosis patients and two controls in Burkina Faso found 60 different bacterial species in patients and 97 in controls, including 45 in common. Further analysis of the results at the individual level indicated seven bacteria, including Enterococcus mundtii and Enterococcus casseliflavus, which were exclusively cultured in controls. Blind quantitative PCR-based exploration of faeces samples in two cohorts in Burkina Faso and in France confirmed a nonsignificant association of E. mundtii and E. casseliflavus with controls. Further in vitro explorations found four E. mundtii and E. casseliflavus strains inhibiting the growth of M. tuberculosis strains representative of four different lineages as well as Mycobacterium africanum, Mycobacterium canettii, and Mycobacterium bovis, in an inoculum-dependent manner. Heat-killed E. mundtii or E. casseliflavus were ineffective. These unprecedented observations of direct interactions between gut E. mundtii and E. casseliflavus with M. tuberculosis complex mycobacteria suggest that gut microbiota may modulate the expression of pulmonary tuberculosis.
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148
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An effective culturomics approach to study the gut microbiota of mammals. Res Microbiol 2020; 171:290-300. [PMID: 32898701 DOI: 10.1016/j.resmic.2020.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023]
Abstract
The microbial characterization of the mammal's gut is an emerging research area, wherein culturomics methodologies applied to human samples are transposed to the animal context without improvement. In this work, using Egyptian mongoose as a model, we explore wet bench conditions to define an effective experimental design based on culturomics and DNA barcoding with potential application to different mammal species. After testing a battery of solid media and enrichments, we show that YCFA-based media, in aerobic and anaerobic conditions, together with PDA supplemented with chloramphenicol, are sufficient to maximize bacterial and fungal microbiota diversity. The pasteurization of the sample enrichment before cultivation is central to gain insight into sporogenic communities. We suggest the application of this optimized culturomics strategy to accurately expand knowledge on the microbial richness of mammals' gut, maximizing the application of common laboratory resources, without dramatic time and consumables expenditure but with high resolution of microbial landscapes. The analysis of ten fecal samples proved adequate to assess the core gastrointestinal microbiota of the mesocarnivore under analysis. This approach may empower most microbiology laboratories, particularly the veterinary, to perform studies on mammal's microbiota, and, in contrast with metagenomics, enabling the recovery of live bacteria for further studies.
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149
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Wilkinson T, Korir D, Ogugo M, Stewart RD, Watson M, Paxton E, Goopy J, Robert C. 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding. Genome Biol 2020; 21:229. [PMID: 32883364 PMCID: PMC7469290 DOI: 10.1186/s13059-020-02144-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 08/16/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The Boran (Bos indicus), indigenous Zebu cattle breed from sub-Saharan Africa, is remarkably well adapted to harsh tropical environments. Due to financial constraints and low-quality forage, African livestock are rarely fed at 100% maintenance energy requirements (MER) and the effect of sub-optimal restricted feeding on the rumen microbiome of African Zebu cattle remains largely unexplored. We collected 24 rumen fluid samples from six Boran cattle fed at sub-optimal and optimal MER levels and characterised their rumen microbial composition by performing shotgun metagenomics and de novo assembly of metagenome-assembled genomes (MAGs). These MAGs were used as reference database to investigate the effect of diet restriction on the composition and functional potential of the rumen microbiome of African cattle. RESULTS We report 1200 newly discovered MAGs from the rumen of Boran cattle. A total of 850 were dereplicated, and their uniqueness confirmed with pairwise comparisons (based on Mash distances) between African MAGs and other publicly available genomes from the rumen. A genome-centric investigation into sub-optimal diets highlighted a statistically significant effect on rumen microbial abundance profiles and a previously unobserved relationship between whole microbiome shifts in functional potential and taxon-level associations in metabolic pathways. CONCLUSIONS This study is the first to identify 1200 high-quality African rumen-specific MAGs and provides further insight into the rumen function in harsh environments with food scarcity. The genomic information from the rumen microbiome of an indigenous African cattle breed sheds light on the microbiome contribution to rumen functionality and constitutes a vital resource in addressing food security in developing countries.
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Affiliation(s)
- Toby Wilkinson
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK
| | - Daniel Korir
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, 00100, Kenya
| | - Moses Ogugo
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, 00100, Kenya
| | - Robert D Stewart
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK
| | - Mick Watson
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK
| | - Edith Paxton
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK
| | - John Goopy
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, 00100, Kenya
| | - Christelle Robert
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK.
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150
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Lee AJ, Einarsson GG, Gilpin DF, Tunney MM. Multi-Omics Approaches: The Key to Improving Respiratory Health in People With Cystic Fibrosis? Front Pharmacol 2020; 11:569821. [PMID: 33013411 PMCID: PMC7509435 DOI: 10.3389/fphar.2020.569821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/17/2020] [Indexed: 12/16/2022] Open
Abstract
The advent of high-throughput multi-omics technologies has underpinned the expansion in lung microbiome research, increasing our understanding of the nature, complexity and significance of the polymicrobial communities harbored by people with CF (PWCF). Having established that structurally complex microbial communities exist within the airways, the focus of recent research has now widened to investigating the function and dynamics of the resident microbiota during disease as well as in health. With further refinement, multi-omics approaches present the opportunity to untangle the complex interplay between microbe-microbe and microbe-host interactions in the lung and the relationship with respiratory disease progression, offering invaluable opportunities to discover new therapeutic approaches for our management of airway infection in CF.
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Affiliation(s)
- Andrew J. Lee
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Gisli G. Einarsson
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Deirdre F. Gilpin
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
| | - Michael M. Tunney
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
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