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Pereira AR, Assis NVD, Paranhos AGDO, Lima DRS, Baeta BEL, Aquino SFD, Silva SDQ. Effect of inoculum composition on the microbial community involved in the anaerobic digestion of sugarcane bagasse. ENVIRONMENTAL TECHNOLOGY 2024; 45:2205-2217. [PMID: 36632771 DOI: 10.1080/09593330.2023.2166877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
In anaerobic digestion (AD), the choice of inoculum type seems to be relevant for methane production for complex substrates, such as lignocellulosic material. Previous work demonstrated that the addition of fresh manure and ruminal fluid to anaerobic sludge improved methane productivity and kinetics of AD of crude sugarcane bagasse (CSB). Considering that the improvement of methane production could be a result of a more adapted microbial community, the present study performed the Next Generation Sequencing analysis to identify changes in the microbiome of anaerobic sludge inoculum, resulting from fresh manure and ruminal fluid addition. In comparison with AD performed only with anaerobic sludge inoculum (50:50, U), accumulated methane production was 15% higher with anaerobic sludge plus ruminal fluid inoculum (50:50, UR) and even higher (68%) with anaerobic sludge with fresh bovine manure inoculum (50:50, UFM), reaching the value of 143 NmLCH4.gVS-1. Clostridium species were highly abundant in all inocula, playing an important role during the hydrolysis and fermentation of CSB, and detoxifying potential inhibitors. Microbial composition also revealed the occurrence of Pseudomonas and Anaerobaculum at UFM inoculum that seem to have contributed to the higher methane production rate, mainly due to their hydrolytic and fermentative ability on lignocellulosic substrates. On the other hand, the presence of Alcaligenes might have had a negative effect on methane production due to their ability to perform methane oxidation.
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Affiliation(s)
- Andressa Rezende Pereira
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | - Nathália Vercelli de Assis
- Graduate Program in Biotechnology, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | | | - Diego Roberto Sousa Lima
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | - Bruno Eduardo Lobo Baeta
- Department of Chemistry, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | | | - Silvana de Queiroz Silva
- Department of Biological Sciences, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
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2
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Wu Y, Zhou T, Gu C, Yin B, Yang S, Zhang Y, Wu R, Wei W. Geographical distribution and species variation of gut microbiota in small rodents from the agro-pastoral transition ecotone in northern China. Ecol Evol 2024; 14:e11084. [PMID: 38469048 PMCID: PMC10926059 DOI: 10.1002/ece3.11084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/03/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
The gut microbiota of rodents is essential for survival and adaptation and is susceptible to various factors, ranging from environmental conditions to genetic predispositions. Nevertheless, few comparative studies have considered the contribution of species identity and geographic spatial distance to variations in the gut microbiota. In this study, a random sampling survey encompassing four rodent species (Apodemus agrarius, Cricetulus barabensis, Tscherskia triton and Rattus norvegicus) was conducted at five sites in northern China's farming-pastoral ecotone. Through a cross-factorial comparison, we aimed to discern whether belonging to the same species or sharing the same capture site predominantly influences the composition of gut microbiota. Notably, the observed variations in microbiome composition among these four rodent species match the host phylogeny at the family level but not at the species level. The gut microbiota of these four rodent species exhibited typical mammalian characteristics, predominantly characterized by the Firmicutes and Bacteroidetes phyla. As the geographic distance between populations increased, the number of shared microbial taxa among conspecific populations decreased. We observed that within a relatively small geographical range, even different species exhibited convergent α-diversity due to their inhabitation within the same environmental microbial pool. In contrast, the composition and structure of the intestinal microbiota in the allopatric populations of A. agrarius demonstrated marked differences, similar to those of C. barabensis. Additionally, geographical environmental elements exhibited significant correlations with diversity indices. Conversely, host-related factors had minimal influence on microbial abundance. Our findings indicated that the similarity of the microbial compositions was not determined primarily by the host species, and the location of the sampling explained a greater amount of variation in the microbial composition, indicating that the local environment played a crucial role in shaping the microbial composition.
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Affiliation(s)
- Yongzhen Wu
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Taoxiu Zhou
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Chen Gu
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Baofa Yin
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Shengmei Yang
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Yunzeng Zhang
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Ruiyong Wu
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Wanhong Wei
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouJiangsuChina
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3
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Pilliol V, Morsli M, Terlier L, Hassani Y, Malat I, Guindo CO, Davoust B, Lamglait B, Drancourt M, Aboudharam G, Grine G, Terrer E. Candidatus Methanosphaera massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos. Microbiol Spectr 2024; 12:e0514122. [PMID: 38189277 PMCID: PMC10845953 DOI: 10.1128/spectrum.05141-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/24/2023] [Indexed: 01/09/2024] Open
Abstract
Methanosphaera stadtmanae was the sole Methanosphaera representative to be cultured and detected by molecular methods in the human gut microbiota, further associated with digestive and respiratory diseases, leaving unknown the actual diversity of human-associated Methanosphaera species. Here, a novel Methanosphaera species, Candidatus Methanosphaera massiliense (Ca. M. massiliense) sp. nov. was isolated by culture using a hydrogen- and carbon dioxide-free medium from one human feces sample. Ca. M. massiliense is a non-motile, 850 nm Gram-positive coccus autofluorescent at 420 nm. Whole-genome sequencing yielded a 29.7% GC content, gapless 1,785,773 bp genome sequence with an 84.5% coding ratio, encoding for alcohol and aldehyde dehydrogenases promoting the growth of Ca. M. massiliense without hydrogen. Screening additional mammal and human feces using a specific genome sequence-derived DNA-polymerase RT-PCR system yielded a prevalence of 22% in pigs, 12% in red kangaroos, and no detection in 149 other human samples. This study, extending the diversity of Methanosphaera in human microbiota, questions the zoonotic sources of Ca. M. massiliense and possible transfer between hosts.IMPORTANCEMethanogens are constant inhabitants in the human gut microbiota in which Methanosphaera stadtmanae was the only cultivated Methanosphaera representative. We grew Candidatus Methanosphaera massiliense sp. nov. from one human feces sample in a novel culture medium under a nitrogen atmosphere. Systematic research for methanogens in human and animal fecal samples detected Ca. M. massiliense in pig and red kangaroo feces, raising the possibility of its zoonotic acquisition. Host specificity, source of acquisition, and adaptation of methanogens should be further investigated.
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Affiliation(s)
- Virginie Pilliol
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Madjid Morsli
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Laureline Terlier
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Yasmine Hassani
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ihab Malat
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Cheick Oumar Guindo
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard Davoust
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | | | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Gérard Aboudharam
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | | | - Elodie Terrer
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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4
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Pilliol V, Beye M, Terlier L, Balmelle J, Kacel I, Lan R, Aboudharam G, Grine G, Terrer E. Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis. Microorganisms 2024; 12:215. [PMID: 38276200 PMCID: PMC10819710 DOI: 10.3390/microorganisms12010215] [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: 12/20/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter piscolens (P. piscolens) in one case of severe periodontitis. Here, reporting on two additional necrotic pulp cases yielded the opportunity to characterise two co-cultivated M. massiliense isolates, both with P. piscolens, as non-motile, 1-2-µm-long and 0.6-0.8-µm-wide Gram-positive coccobacilli which were autofluorescent at 420 nm. The two whole genome sequences featured a 31.3% GC content, gapless 1,834,388-base-pair chromosome exhibiting an 85.9% coding ratio, encoding a formate dehydrogenase promoting M. massiliense growth without hydrogen in GG medium. These data pave the way to understanding a symbiotic, transkingdom association with P. piscolens and its role in oral pathologies.
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Affiliation(s)
- Virginie Pilliol
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
| | - Mamadou Beye
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Laureline Terlier
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Julien Balmelle
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Idir Kacel
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Romain Lan
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
- CNRS, EFS, ADES, Aix-Marseille University, 13385 Marseille, France
| | - Gérard Aboudharam
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
| | - Ghiles Grine
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Elodie Terrer
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
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5
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Aryee G, Luecke SM, Dahlen CR, Swanson KC, Amat S. Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle. Microorganisms 2023; 11:2746. [PMID: 38004757 PMCID: PMC10673468 DOI: 10.3390/microorganisms11112746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.
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Affiliation(s)
- Godson Aryee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Kendall C. Swanson
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
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Meene A, Gierse L, Schwaiger T, Karte C, Schröder C, Höper D, Wang H, Groß V, Wünsche C, Mücke P, Kreikemeyer B, Beer M, Becher D, Mettenleiter TC, Riedel K, Urich T. Archaeome structure and function of the intestinal tract in healthy and H1N1 infected swine. Front Microbiol 2023; 14:1250140. [PMID: 37779690 PMCID: PMC10534045 DOI: 10.3389/fmicb.2023.1250140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Background Methanogenic archaea represent a less investigated and likely underestimated part of the intestinal tract microbiome in swine. Aims/Methods This study aims to elucidate the archaeome structure and function in the porcine intestinal tract of healthy and H1N1 infected swine. We performed multi-omics analysis consisting of 16S rRNA gene profiling, metatranscriptomics and metaproteomics. Results and discussion We observed a significant increase from 0.48 to 4.50% of archaea in the intestinal tract microbiome along the ileum and colon, dominated by genera Methanobrevibacter and Methanosphaera. Furthermore, in feces of naïve and H1N1 infected swine, we observed significant but minor differences in the occurrence of archaeal phylotypes over the course of an infection experiment. Metatranscriptomic analysis of archaeal mRNAs revealed the major methanogenesis pathways of Methanobrevibacter and Methanosphaera to be hydrogenotrophic and methyl-reducing, respectively. Metaproteomics of archaeal peptides indicated some effects of the H1N1 infection on central metabolism of the gut archaea. Conclusions/Take home message Finally, this study provides the first multi-omics analysis and high-resolution insights into the structure and function of the porcine intestinal tract archaeome during a non-lethal Influenza A virus infection of the respiratory tract, demonstrating significant alterations in archaeal community composition and central metabolic functions.
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Affiliation(s)
- Alexander Meene
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Laurin Gierse
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | | | | | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Verena Groß
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Pierre Mücke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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7
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Naud S, Valles C, Abdillah A, Abou Chacra L, Mekhalif FZ, Ibrahim A, Caputo A, Baudoin JP, Gouriet F, Bittar F, Lagier JC, Ranque S, Fenollar F, Tidjani Alou M, Raoult D. Preliminary landscape of Candidatus Saccharibacteria in the human microbiome. Front Cell Infect Microbiol 2023; 13:1195679. [PMID: 37577371 PMCID: PMC10414567 DOI: 10.3389/fcimb.2023.1195679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date. Methods In this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics. Results Using Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples. Conclusion This study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.
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Affiliation(s)
- Sabrina Naud
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Camille Valles
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Abdourahim Abdillah
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Linda Abou Chacra
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Fatima Zouina Mekhalif
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Ahmad Ibrahim
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Aurelia Caputo
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Pierre Baudoin
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Frédérique Gouriet
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Fadi Bittar
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Stéphane Ranque
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Florence Fenollar
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Maryam Tidjani Alou
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
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8
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Cisek AA, Dolka B, Bąk I, Cukrowska B. Microorganisms Involved in Hydrogen Sink in the Gastrointestinal Tract of Chickens. Int J Mol Sci 2023; 24:ijms24076674. [PMID: 37047647 PMCID: PMC10095559 DOI: 10.3390/ijms24076674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Hydrogen sink is a beneficial process, which has never been properly examined in chickens. Therefore, the aim of this study was to assess the quantity and quality of microbiota involved in hydrogen uptake with the use of real-time PCR and metagenome sequencing. Analyses were carried out in 50 free-range chickens, 50 commercial broilers, and 54 experimental chickens isolated from external factors. The median values of acetogens, methanogens, sulfate-reducing bacteria (SRB), and [NiFe]-hydrogenase utilizers measured in the cecum were approx. 7.6, 0, 0, and 3.2 log10/gram of wet weight, respectively. For the excreta samples, these values were 5.9, 4.8, 4, and 3 log10/gram of wet weight, respectively. Our results showed that the acetogens were dominant over the other tested groups of hydrogen consumers. The quantities of methanogens, SRB, and the [NiFe]-hydrogenase utilizers were dependent on the overall rearing conditions, being the result of diet, environment, agrotechnical measures, and other factors combined. By sequencing of the 16S rRNA gene, archaea of the genus Methanomassiliicoccus (Candidatus Methanomassiliicoccus) were discovered in chickens for the first time. This study provides some indication that in chickens, acetogenesis may be the main metabolic pathway responsible for hydrogen sink.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Beata Dolka
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences, St. Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Iwona Bąk
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, St. Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Bożena Cukrowska
- Department of Pathology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
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9
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Guerra V, Tiago I, Aires A, Coelho C, Nunes J, Martins LO, Veríssimo A. The gastrointestinal microbiome of browsing goats (Capra hircus). PLoS One 2022; 17:e0276262. [PMID: 36251671 PMCID: PMC9576075 DOI: 10.1371/journal.pone.0276262] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/04/2022] [Indexed: 11/25/2022] Open
Abstract
Despite the growing interest in the ruminants' gastrointestinal tract (GIT) microbiomes' ability to degrade plant materials by animal husbandry and industrial sectors, only a few studies addressed browsing ruminants. The present work describes the taxonomic and functional profile of the bacterial and archaeal communities from five different gastrointestinal sections (rumen, omasum-abomasum, jejunum, cecum and colon) of browsing Capra hircus, by metabarcoding using 16S rRNA genes hypervariable regions. The bacterial communities across the GITs are mainly composed of Bacillota and Bacteroidota. Prevotella was the leading bacterial group found in the stomachs, Romboutsia in the jejuna, and Rikenellaceae_RC9_gut_group, Bacteroides, UCG-010_ge, UCG-005, and Alistipes in large intestines. The archaeal communities in the stomachs and jejuna revealed to be mainly composed of Methanobrevibacter, while in the large intestines its dominance is shared with Methanocorpusculum. Across the GITs, the main metabolic functions were related to carbohydrate, amino acid, and energy metabolisms. Significant differences in the composition and potential biological functions of the bacterial communities were observed among stomachs, jejuna and large intestines. In contrast, significant differences were observed among stomachs and jejuna verse large intestines for archaeal communities. Overall different regions of the GIT are occupied by different microbial communities performing distinct biological functions. A high variety of glycoside hydrolases (GHs) indispensable for degrading plant cell wall materials were predicted to be present in all the GIT sections.
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Affiliation(s)
- Vera Guerra
- Department of Life Sciences, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Centre Bio R&D Unit, Association BLC3—Technology and Innovation Campus, Lagares da Beira, Oliveira do Hospital, Portugal
| | - Igor Tiago
- Department of Life Sciences, Centre for Functional Ecology–Science for People and the Planet, University of Coimbra, Coimbra, Portugal
| | - Aitana Aires
- Department of Life Sciences, Centre for Functional Ecology–Science for People and the Planet, University of Coimbra, Coimbra, Portugal
- FitoLab, Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Catarina Coelho
- Department of Life Sciences, Centre for Functional Ecology–Science for People and the Planet, University of Coimbra, Coimbra, Portugal
| | - João Nunes
- Centre Bio R&D Unit, Association BLC3—Technology and Innovation Campus, Lagares da Beira, Oliveira do Hospital, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia e Química Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - António Veríssimo
- Department of Life Sciences, Centre for Functional Ecology–Science for People and the Planet, University of Coimbra, Coimbra, Portugal
- * E-mail:
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10
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Rice bran in old horse’s nutrition and their influence on condition, blood biochemical parameters, total feces bacteria and methanogen population. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
This study aimed to verify whether the inclusion of 0.5 kg full-fat rice bran per day in the diet of geriatric horses will improve their condition, increase the population of methanogens in the cecum, and thus affect the biochemical blood parameters. The experiment assumed 2 research periods: 6 healthy, non-working horses over 20 years of age (480 ± 20 kg of body weight) were fed only hay (±8.86 kg/day/head) in the first period and hay (±8.00 kg/day/head) and rice bran (0.5 kg/day/head) in the second one. Each of these periods lasted 4 months. The Body Condition Scoring (BCS) assessment was performed at the beginning and end of the experiment. Blood and feces samples were collected on the first and last day of each period. After feeding with the addition of rice bran, BCS increased by 1.17 units on a 9-point scale. The experiment showed an increase in the total number of bacteria and methanogens inhabiting the cecum of horses. This can lead to better digestion of carbohydrates, absorption of nutrients, and, consequently, increased body weight. No differences occurred in the hematology and serum biochemistry indices of horses fed a diet including rice bran, except for the amount of serum globulin and the albumin to globulin ratio. Rice bran affected essential serum fatty acid profile (increased PUFA and decreased MUFA) which confirmed the possibility to use diet as a serum fatty acids profile modulator.
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11
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Guindo CO, Amir L, Couderc C, Drancourt M, Grine G. Rapid identification of clinically interesting methanogens using an improved MALDI-TOF-MS assay. Access Microbiol 2022; 4:acmi000372. [PMID: 36003219 PMCID: PMC9394734 DOI: 10.1099/acmi.0.000372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
Methanogens, the archaea uniquely detoxifying fermentative hydrogen into methane in the digestive tract, are increasingly being detected in pathology situations, rendering their rapid identification mandatory. We improved the experimental protocol to identify broth-cultured methanogens by matrix-assisted laser desorption time-of-flight MS (MALDI-TOF-MS). A database incorporating 34 reference spectra derived from 16 methanogen reference strains representative of eight species supported further identification of 21 Methanobrevibacter smithii and 14 Methanobrevibacter oralis isolates broth-cultured from human stool and oral fluid, respectively, with scores >2. In addition, MALDI-TOF-MS differentiated five Methanobrevibacter smithii genotypes incorporated in the study. The data reported here found MALDI-TOF-MS as a first-line identification method for methanogens recovered from microbiota and clinical samples.
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Affiliation(s)
- Cheick Oumar Guindo
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Lynda Amir
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Carine Couderc
- Laboratoire de Microbiologie, Assistance Publique à Marseille, IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- Laboratoire de Microbiologie, Assistance Publique à Marseille, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ghiles Grine
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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12
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Sereme Y, Michel M, Mezouar S, Guindo CO, Kaba L, Grine G, Mura T, Mège JL, Tran TA, Corbeau P, Filleron A, Vitte J. A Non-Invasive Neonatal Signature Predicts Later Development of Atopic Diseases. J Clin Med 2022; 11:jcm11102749. [PMID: 35628877 PMCID: PMC9143112 DOI: 10.3390/jcm11102749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Preterm birth is a major cause of morbidity and mortality in infants and children. Non-invasive methods for screening the neonatal immune status are lacking. Archaea, a prokaryotic life domain, comprise methanogenic species that are part of the neonatal human microbiota and contribute to early immune imprinting. However, they have not yet been characterized in preterm neonates. Objective: To characterize the gut immunological and methanogenic Archaeal (MA) signature in preterm neonates, using the presence or absence of atopic conditions at the age of one year as a clinical endpoint. Methods: Meconium and stool were collected from preterm neonates and used to develop a standardized stool preparation method for the assessment of mediators and cytokines and characterize the qPCR kinetics of gut MA. Analysis addressed the relationship between immunological biomarkers, Archaea abundance, and atopic disease at age one. Results: Immunoglobulin E, tryptase, calprotectin, EDN, cytokines, and MA were detectable in the meconium and later samples. Atopic conditions at age of one year were positively associated with neonatal EDN, IL-1β, IL-10, IL-6, and MA abundance. The latter was negatively associated with neonatal EDN, IL-1β, and IL-6. Conclusions: We report a non-invasive method for establishing a gut immunological and Archaeal signature in preterm neonates, predictive of atopic diseases at the age of one year.
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Affiliation(s)
- Youssouf Sereme
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
| | - Moïse Michel
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
- Immunology Department, University Hospital Nîmes, 30900 Nîmes, France
| | - Soraya Mezouar
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
| | - Cheick Oumar Guindo
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
| | - Lanceï Kaba
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, AP-HM, SSA, VITROME, Aix-Marseille Université, 13284 Marseille, France
| | - Ghiles Grine
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
- UFR Odontologie, Aix-Marseille Université, 13284 Marseille, France
| | - Thibault Mura
- INSERM, University of Montpellier, U1061, Neuropsychiatry: Epidemiological and Clinical Research, 34093 Montpellier, France;
- Laboratoire de Biostatistique, Epidémiologie Clinique, Santé Publique Innovation et Méthodologie (BESPIM), Groupe Hospitalier Caremeau, CHU de Nîmes, Nîmes University Hospital, 30900 Nîmes, France
| | - Jean-Louis Mège
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
| | - Tu Anh Tran
- Paediatrics Department, University Hospital Nîmes, 30900 Nîmes, France;
- INSERM U1183, Institute for Regenerative Medicine & Biotherapy, 34295 Montpellier, France
- Faculty de Medicine, Montpellier University, 34000 Montpellier, France
| | - Pierre Corbeau
- Immunology Department, University Hospital Nîmes, 30900 Nîmes, France
- Faculty de Medicine, Montpellier University, 34000 Montpellier, France
- CNRS UMR 9002, Institute of Human Genetics, 34090 Montpellier, France
- Correspondence: (P.C.); (A.F.); (J.V.); Tel.: +33-4-13-73-20-51 (J.V.); Fax: +33-4-13-73-20-52 (J.V.)
| | - Anne Filleron
- Paediatrics Department, University Hospital Nîmes, 30900 Nîmes, France;
- INSERM U1183, Institute for Regenerative Medicine & Biotherapy, 34295 Montpellier, France
- Faculty de Medicine, Montpellier University, 34000 Montpellier, France
- Correspondence: (P.C.); (A.F.); (J.V.); Tel.: +33-4-13-73-20-51 (J.V.); Fax: +33-4-13-73-20-52 (J.V.)
| | - Joana Vitte
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
- Faculty de Medicine, Montpellier University, 34000 Montpellier, France
- IDESP, INSERM UMR UA11, Institut Desbrest d’Epidemiologie et de Santé Publique (IDESP) Campus Sante, 34093 Montpellier, France
- Correspondence: (P.C.); (A.F.); (J.V.); Tel.: +33-4-13-73-20-51 (J.V.); Fax: +33-4-13-73-20-52 (J.V.)
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13
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Deng F, Peng Y, Zhang Z, Howe S, Wu Z, Dou J, Li Y, Wei X, Wang X, Liang Y, Zhao J, Li Y. Weaning Time Affects the Archaeal Community Structure and Functional Potential in Pigs. Front Microbiol 2022; 13:845621. [PMID: 35387077 PMCID: PMC8979004 DOI: 10.3389/fmicb.2022.845621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Archaea are considered a “keystone” of the gut microbiome and are linked with the host’s energy harvest and health. Although a few studies have investigated the gut archaea in pigs, especially piglets, little is known about the effects of weaning on archaeal structure and function. In this study, we explored the effects of weaning on the longitudinal changes of archaeal composition, diversity, and functional potential in pigs overtime by re-analyzing a recently published metagenomic dataset that included 176 fecal samples collected from commercial pigs on days 7, 14, 21, 28, 35, 70, and 140 after birth. Overall, the richness and diversity of archaeal species showed an increasing trend, and weaning significantly affected the richness of archaeal species. Methanobrevibacter A smithii significantly decreased and was replaced by Methanobrevibacter A sp900769095 within 2 weeks after weaning. For the functional potential, the richness of KEGG KOs increased over time. LEfSe analysis identified 18 KOs, including for example, ko04623 (cytosolic DNA-sensing pathway), ko00500 (starch and sucrose metabolism), and so on, significantly enriched in the weaning pigs, suggesting the involvement of archaea in the piglets’ adaptation to the new diet after weaning. Correlation analysis based on Random Forest regression and Pearson correlation showed that archaeal species richness was significantly associated with pig bodyweight on both days 70 and 140. Methanobrevibacter A sp900769095 (R = 0.405, p = 0.040) and Methanobrevibacter A smithii (R = 0.535, p = 0.004) were positively linked with pigs’ bodyweight on days 70 and 140, respectively. Our results revealed the dynamic changes of archaeal diversity and functions and demonstrated the effects of weaning on the gut archaea of pigs, suggesting archaea might play essential roles in swine nutrition, metabolism, and growth performance, especially during the critical weaning process.
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Affiliation(s)
- Feilong Deng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Yunjuan Peng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Zhihao Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Samantha Howe
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Zhuosui Wu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Jieying Dou
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Yuling Li
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Xiaoyuan Wei
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Xiaofan Wang
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Yong Liang
- Institute of Systems Engineering, Macau University of Science and Technology, Macau, China.,The Peng Cheng Laboratory, Shenzhen, China
| | - Jiangchao Zhao
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
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14
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Medina-Chávez NO, Travisano M. Archaeal Communities: The Microbial Phylogenomic Frontier. Front Genet 2022; 12:693193. [PMID: 35154237 PMCID: PMC8826477 DOI: 10.3389/fgene.2021.693193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Archaea are a unique system for investigating the diversity of life. There are the most diverse group of organisms with the longest evolutionary history of life on Earth. Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life. They exist in the harshest environments and benign conditions, providing a system to investigate the basis for living in extreme environments. They are frequently members of microbial communities, albeit generally rare. Archaea were central in the evolution of Eukaryotes and can be used as a proxy for studying life on other planets. Future advances will depend not only upon phylogenomic studies but also on a better understanding of isolation and cultivation techniques.
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Affiliation(s)
- Nahui Olin Medina-Chávez
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Michael Travisano
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN, United States
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15
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Guindo CO, Morsli M, Bellali S, Drancourt M, Grine G. A Tetragenococcus halophilus human gut isolate. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100112. [PMID: 35243447 PMCID: PMC8866149 DOI: 10.1016/j.crmicr.2022.100112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 10/28/2022] Open
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16
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Sereme Y, Guindo CO, Filleron A, Corbeau P, Tran TA, Drancourt M, Vitte J, Grine G. Meconial Methanobrevibacter smithii suggests intrauterine methanogen colonization in preterm neonates. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100034. [PMID: 34841325 PMCID: PMC8610290 DOI: 10.1016/j.crmicr.2021.100034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/13/2022] Open
Abstract
The first ever detection in the meconium of the methanogen M. smithii. These data position M. smithii among the early inhabitants of the human gut. These data suggest the contribution of methanogens to the perinatal development of intestinal microbiota and physiology.
To understand the dynamics of methanogens in the human intestinal microbiota, we investigated the presence of methanogens in meconium using a polyphasic approach including microscopy and PCR-sequencing in 33 meconium samples collected from 33 pre-term neonates, in accordance with current ethics regulation. In the presence of negative controls, 90.9% samples were real-time PCR-positive for methanogens and 69.7 % were PCR-sequencing positive, identified as Methanobrevibacter (M.) smithii. Further, auto-fluorescent analysis detected methanogens in the two meconium samples analyzed, with a morphology suggesting M. smithii. Multispacer Sequence Typing found M. smithii genotypes ST1 and ST2, previously described as intestinal microbiota inhabitants. C-section delivery and non-use of peripartum antibiotics significantly correlated with PCR-detection of methanogens in meconium. These data position M. smithii among the early inhabitants of the human gut, detectable immediately after birth and suggest the contribution of methanogens to the perinatal development of intestinal microbiota and physiology.
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Affiliation(s)
- Youssouf Sereme
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Cheick Oumar Guindo
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Anne Filleron
- Department of Pediatrics, CHU Nîmes, Univ Montpellier, Nîmes, France
- IRMB, Univ Montpellier, INSERM, Montpellier, France
| | - Pierre Corbeau
- Montpellier University, Montpellier, France
- Immunology Department, University Hospital, Nîmes, France
- CNRS UMR9002, Institute of Human Genetics, Montpellier, France
| | - Tu Anh Tran
- Department of Pediatrics, CHU Nîmes, Univ Montpellier, Nîmes, France
- IRMB, Univ Montpellier, INSERM, Montpellier, France
- Montpellier University, Montpellier, France
| | - Michel Drancourt
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Univ, APHM, Hôpital Timone, Service de Bactériologie- Epidémiologie- Hygiène hospitalière, Marseille, France
| | - Joana Vitte
- IDESP, INSERM UMR UA11, Montpellier University, Montpellier, France
| | - Ghiles Grine
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, UFR Odontologie, Marseille, France
- Corresponding author.
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17
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Ghosh S, Pramanik S. Structural diversity, functional aspects and future therapeutic applications of human gut microbiome. Arch Microbiol 2021; 203:5281-5308. [PMID: 34405262 PMCID: PMC8370661 DOI: 10.1007/s00203-021-02516-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023]
Abstract
The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host's cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut-brain-immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.
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Affiliation(s)
- Soma Ghosh
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute, i-8 Sector-C, East Kolkata Township, Kolkata, 700107, India.
| | - Sreemanta Pramanik
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute, i-8 Sector-C, East Kolkata Township, Kolkata, 700107, India
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18
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Hu D, Yang J, Qi Y, Li B, Li K, Mok KM. Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment. Front Vet Sci 2021; 8:708512. [PMID: 34490397 PMCID: PMC8416479 DOI: 10.3389/fvets.2021.708512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022] Open
Abstract
Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to determine the corresponding changes of their functional attributes based on metagenomic sequencing. Results showed that in archaea, the methanogen of Euryarchaeota was the dominant phylum. Under this phylum, anthelmintic treatment increased the Methanobrevibacter genus and decreased the Methanocorpusculum genus and two other dominant archaea species, Methanocorpusculum labreanum and Methanocorpusculum bavaricum. In bacteria, Firmicutes and Bacteroidetes were the dominant phyla. Anthelmintic treatment increased the genera of Clostridium and Eubacterium and decreased those of Bacteroides and Prevotella and dominant bacteria species. These altered genera were associated with immunity and digestion. In eukaryota, anthelmintic treatment also changed the genera related to digestion and substantially decreased the relative abundances of identified species. In virus, anthelmintic treatment increased the genus of unclassified_d__Viruses and decreased those of unclassified_f__Siphoviridae and unclassified_f__Myoviridae. Most of the identified viral species were classified into phage, which were more sensitive to anthelmintic treatment than other viruses. Furthermore, anthelmintic treatment was found to increase the number of pathogens related to some clinical diseases in horses. The COG and KEGG function analysis showed that the intestinal microbiota of Przewalski's horse mainly participated in the carbohydrate and amino acid metabolism. The anthelmintic treatment did not change their overall function; however, it displaced the population of the functional microbes involved in each function or pathway. These results provide a complete view on the changes caused by anthelmintic treatment in the intestinal microbiota of the Przewalski's horses.
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Affiliation(s)
- Dini Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jianming Yang
- Xinjiang Research Centre for Breeding Przewalski's Horse, Urumqi, China
| | - Yingjie Qi
- Xinjiang Kalamaili Ungulate Nature Reserve Management Center, Changji, China
| | - Boling Li
- China National Environment Monitoring Centre, Beijing, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Kai Meng Mok
- Department of Civil and Environmental Engineering, University of Macau, Macao, China
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