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Ahmad A, Ashfaq M, Rashid M. Editorial: The intricate web of gastrointestinal virome, mycome and archaeome: implications for gastrointestinal diseases. Front Genet 2024; 15:1463350. [PMID: 39184347 PMCID: PMC11341467 DOI: 10.3389/fgene.2024.1463350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 07/30/2024] [Indexed: 08/27/2024] Open
Affiliation(s)
- Asrar Ahmad
- Center for Sickle Cell Disease, Howard University, Washington, DC, United States
| | - Mohammad Ashfaq
- The University Centre for Research and Development (UCRD), Chandigarh University, Mohali, Punjab, India
| | - Mudasir Rashid
- Department of Medicine and Cancer Center, Howard University, Washington, DC, United States
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2
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Duller S, Moissl-Eichinger C. Archaea in the Human Microbiome and Potential Effects on Human Infectious Disease. Emerg Infect Dis 2024; 30. [PMID: 39043386 PMCID: PMC11286065 DOI: 10.3201/eid3008.240181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
Archaea represent a separate domain of life, next to bacteria and eukarya. As components of the human microbiome, archaea have been associated with various diseases, including periodontitis, endodontic infections, small intestinal bacterial overgrowth, and urogenital tract infections. Archaea are generally considered nonpathogenic; the reasons are speculative because of limited knowledge and gene annotation challenges. Nevertheless, archaeal syntrophic principles that shape global microbial networks aid both archaea and potentially pathogenic bacteria. Evaluating archaea interactions remains challenging, requiring clinical studies on inflammatory potential and the effects of archaeal metabolism. Establishing a culture collection is crucial for investigating archaea functions within the human microbiome, which could improve health outcomes in infectious diseases. We summarize potential reasons for archaeal nonpathogenicity, assess the association with infectious diseases in humans, and discuss the necessary experimental steps to enable mechanistic studies involving archaea.
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3
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Poupin MJ, González B. Embracing complexity in plant-microbiome systems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70000. [PMID: 39189551 PMCID: PMC11348195 DOI: 10.1111/1758-2229.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/27/2024] [Indexed: 08/28/2024]
Abstract
Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.
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Affiliation(s)
- María Josefina Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
| | - Bernardo González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
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4
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Polêto M, Allen KD, Lemkul JA. Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F 430 Modifications. Biochemistry 2024; 63:1783-1794. [PMID: 38914925 PMCID: PMC11256747 DOI: 10.1021/acs.biochem.4c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024]
Abstract
Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in methanogens and anaerobic methanotrophs (ANME), respectively. The prosthetic group of MCR is coenzyme F430, a nickel-containing tetrahydrocorphin. Several modified versions of F430 have been discovered, including the 172-methylthio-F430 (mtF430) used by ANME-1 MCR. Here, we employ molecular dynamics (MD) simulations to investigate the active site dynamics of MCR from Methanosarcina acetivorans and ANME-1 when bound to the canonical F430 compared to 172-thioether coenzyme F430 variants and substrates (methyl-coenzyme M and coenzyme B) for methane formation. Our simulations highlight the importance of the Gln to Val substitution in accommodating the 172 methylthio modification in ANME-1 MCR. Modifications at the 172 position disrupt the canonical substrate positioning in M. acetivorans MCR. However, in some replicates, active site reorganization to maintain substrate positioning suggests that the modified F430 variants could be accommodated in a methanogenic MCR. We additionally report the first quantitative estimate of MCR intrinsic electric fields that are pivotal in driving methane formation. Our results suggest that the electric field aligned along the CH3-S-CoM thioether bond facilitates homolytic bond cleavage, coinciding with the proposed catalytic mechanism. Structural perturbations, however, weaken and misalign these electric fields, emphasizing the importance of the active site structure in maintaining their integrity. In conclusion, our results deepen the understanding of MCR active site dynamics, the enzyme's organizational role in intrinsic electric fields for catalysis, and the interplay between active site structure and electrostatics.
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Affiliation(s)
- Marcelo
D. Polêto
- Department of Biochemistry, Virginia Tech, 111 Engel Hall, 340 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Kylie D. Allen
- Department of Biochemistry, Virginia Tech, 111 Engel Hall, 340 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Justin A. Lemkul
- Department of Biochemistry, Virginia Tech, 111 Engel Hall, 340 West Campus Drive, Blacksburg, Virginia 24061, United States
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5
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Agnew A, Humm E, Zhou K, Gunsalus RP, Zhou ZH. Reconstruction and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602819. [PMID: 39026688 PMCID: PMC11257533 DOI: 10.1101/2024.07.09.602819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5'-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryoEM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryoEM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37 amino acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.
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Neumann CJ, Pausan MR, Haid V, Weiss EC, Kolovetsiou-Kreiner V, Amtmann B, Winkler P, Mahnert A, Jantscher-Krenn E, Moissl-Eichinger C. The dynamics of the female microbiome: unveiling abrupt changes of microbial domains across body sites from prepartum to postpartum phases. Microbiol Spectr 2024; 12:e0014724. [PMID: 38917430 PMCID: PMC11302012 DOI: 10.1128/spectrum.00147-24] [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: 01/16/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024] Open
Abstract
The microbial ecosystem of women undergoes enormous changes during pregnancy and the perinatal period. Little is known about the extent of changes in the maternal microbiome beyond the vaginal cavity and its recovery after birth. In this study, we followed pregnant women [maternal prepartum (mpre), n = 30] into the postpartum period [1 month postpartum, maternal postpartum (mpost), n = 30]. We profiled their oral, urinary, and vaginal microbiome; archaeome; mycobiome; and urinary metabolome and compared them with those of nonpregnant (np) women (n = 29). Overall, pregnancy status (np, mpre, and mpost) had a smaller effect on the microbiomes than body site, but massive transitions were observed for the oral and urogenital (vaginal and urinary) microbiomes. While the oral microbiome fluctuates during pregnancy but stabilizes rapidly within the first month postpartum, the urogenital microbiome is characterized by a major remodeling caused by a massive loss of Lactobacillus and thus a shift from Vaginal Community State Type (CST) I (40% of women) to CST IV (85% of women). The urinary metabolome rapidly reached an np-like composition after delivery, apart from lactose and oxaloacetic acid, which were elevated during active lactation. Fungal and archaeal profiles were indicative of pregnancy status. Methanobacterium signatures were found mainly in np women, and Methanobrevibacter showed an opposite behavior in the oral cavity (increased) and vagina (decreased) during pregnancy. Our findings suggest that the massive remodeling of the maternal microbiome and metabolome needs more attention and that potential interventions could be envisioned to optimize recovery and avoid long-term effects on maternal health and subsequent pregnancies. IMPORTANCE The perinatal microbiome is of specific interest for the health of the mother and infant. We therefore investigate the dynamics of the female microbiome from nonpregnant over prepartum to the postpartum period in urine and the oral and vaginal cavities. A specific focus of this study is put not only on the bacterial part of the microbiome but also on the underinvestigated contribution of fungi and archaea. To our knowledge, we present the first study highlighting those aspects. Our findings suggest that the massive remodeling of the maternal microbiome and metabolome needs more attention and that potential interventions could be envisioned to optimize recovery and avoid long-term effects on maternal health and subsequent pregnancies.
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Affiliation(s)
- Charlotte J. Neumann
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Manuela-Raluca Pausan
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Victoria Haid
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Eva-Christine Weiss
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
| | | | - Bettina Amtmann
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
| | - Petra Winkler
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Evelyn Jantscher-Krenn
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Graz, Styria, Austria
- BioTechMed, Graz, Styria, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
- BioTechMed, Graz, Styria, Austria
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7
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Mukhopadhyay B. A reminder-peptidoglycan cell walls indeed occur in the archaeal domain, specifically in the members of Methanobacteria and Methanopyri classes. Front Microbiol 2024; 15:1329047. [PMID: 38784805 PMCID: PMC11111885 DOI: 10.3389/fmicb.2024.1329047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/27/2024] [Indexed: 05/25/2024] Open
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8
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Cena JAD, Belmok A, Kyaw CM, Dame-Teixeira N. The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry. Arch Oral Biol 2024; 161:105936. [PMID: 38422909 DOI: 10.1016/j.archoralbio.2024.105936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases. DESIGN This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites. RESULTS Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla. CONCLUSIONS Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.
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Affiliation(s)
| | - Aline Belmok
- Institute of Biology, University of Brasilia, Brazil
| | | | - Naile Dame-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brazil; Division of Oral Biology, School of Dentistry, University of Leeds, UK.
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Alshareef SA. Metabolic analysis of the CAZy class glycosyltransferases in rhizospheric soil fungiome of the plant species Moringa oleifera. Saudi J Biol Sci 2024; 31:103956. [PMID: 38404538 PMCID: PMC10891331 DOI: 10.1016/j.sjbs.2024.103956] [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: 01/20/2024] [Revised: 02/03/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
The target of the present work is to study the most abundant carbohydrate-active enzymes (CAZymes) of glycosyltransferase (GT) class, which are encoded by fungiome genes present in the rhizospheric soil of the plant species Moringa oleifera. The datasets of this CAZy class were recovered using metagenomic whole shotgun genome sequencing approach, and the resultant CAZymes were searched against the KEGG pathway database to identify function. High emphasis was given to the two GT families, GT4 and GT2, which were the highest within GT class in the number and abundance of gene queries in this soil compartment. These two GT families harbor CAZymes playing crucial roles in cell membrane and cell wall processes. These CAZymes are responsible for synthesizing essential structural components such as cellulose and chitin, which contribute to the integrity of cell walls in plants and fungi. The CAZyme beta-1,3-glucan synthase of GT2 family accumulates 1,3-β-glucan, which provides elasticity as well as tensile strength to the fungal cell wall. Other GT CAZymes contribute to the biosynthesis of several compounds crucial for cell membrane and wall integrity, including lipopolysaccharide, e.g., lipopolysaccharide N-acetylglucosaminyltransferase, cell wall teichoic acid, e.g., alpha-glucosyltransferase, and cellulose, e.g., cellulose synthase. These compounds also play pivotal roles in ion homeostasis, organic carbon mineralization, and osmoprotection against abiotic stresses in plants. This study emphasizes the major roles of these two CAZy GT families in connecting the structure and function of cell membranes and cell walls of fungal and plant cells. The study also sheds light on the potential occurrence of tripartite symbiotic relationships involving the plant, rhizospheric bacteriome, and fungiome via the action of CAZymes of GT4 and GT2 families. These findings provide valuable insights towards the generation of innovative agricultural practices to enhance the performance of crop plants in the future.
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Affiliation(s)
- Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
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10
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Kuehnast T, Kumpitsch C, Mohammadzadeh R, Weichhart T, Moissl-Eichinger C, Heine H. Exploring the human archaeome: its relevance for health and disease, and its complex interplay with the human immune system. FEBS J 2024. [PMID: 38555566 DOI: 10.1111/febs.17123] [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: 11/03/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
This Review aims to coalesce existing knowledge on the human archaeome, a less-studied yet critical non-bacterial component of the human microbiome, with a focus on its interaction with the immune system. Despite a largely bacteria-centric focus in microbiome research, archaea present unique challenges and opportunities for understanding human health. We examine the archaeal distribution across different human body sites, such as the lower gastrointestinal tract (LGT), upper aerodigestive tract (UAT), urogenital tract (UGT), and skin. Variability in archaeal composition exists between sites; methanogens dominate the LGT, while Nitrososphaeria are prevalent on the skin and UAT. Archaea have yet to be classified as pathogens but show associations with conditions such as refractory sinusitis and vaginosis. In the LGT, methanogenic archaea play critical metabolic roles by converting bacterial end-products into methane, correlating with various health conditions, including obesity and certain cancers. Finally, this work looks at the complex interactions between archaea and the human immune system at the molecular level. Recent research has illuminated the roles of specific archaeal molecules, such as RNA and glycerolipids, in stimulating immune responses via innate immune receptors like Toll-like receptor 8 (TLR8) and 'C-type lectin domain family 4 member E' (CLEC4E; also known as MINCLE). Additionally, metabolic by-products of archaea, specifically methane, have demonstrated immunomodulatory effects through anti-inflammatory and anti-oxidative pathways. Despite these advancements, the mechanistic underpinnings of how archaea influence immune activity remain a fertile area for further investigation.
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Affiliation(s)
- Torben Kuehnast
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Christina Kumpitsch
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Rokhsareh Mohammadzadeh
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Thomas Weichhart
- Institute of Medical Genetics, Medical University of Vienna, Austria
| | - Christine Moissl-Eichinger
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
- BioTechMed Graz, Austria
| | - Holger Heine
- Research Center Borstel - Leibniz Lung Center, Division of Innate Immunity, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
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Kushkevych I, Martínková K, Mráková L, Giudici F, Baldi S, Novak D, Gajdács M, Vítězová M, Dordevic D, Amedei A, Rittmann SKMR. Comparison of microbial communities and the profile of sulfate-reducing bacteria in patients with ulcerative colitis and their association with bowel diseases: a pilot study. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:79-89. [PMID: 38486888 PMCID: PMC10939707 DOI: 10.15698/mic2024.03.817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 03/17/2024]
Abstract
Considerable evidence has accumulated regarding the molecular relationship between gut microbiota (GM) composition and the onset (clinical presentation and prognosis of ulcerative colitis (UC)). In addition, it is well documented that short-chain fatty acid (SCFA)-producing bacteria may play a fundamental role in maintaining an anti-inflammatory intestinal homeostasis, but sulfate- and sulfite reducing bacteria may be responsible for the production of toxic metabolites, such as hydrogen sulfide and acetate. Hence, the present study aimed to assess the GM composition - focusing on sulfate-reducing bacteria (SRB) - in patients with severe, severe-active and moderate UC. Each one of the six enrolled patients provided two stool samples in the following way: one sample was cultivated in a modified SRB-medium before 16S rRNA sequencing and the other was not cultivated. Comparative phylogenetic analysis was conducted on each sample. Percentage of detected gut microbial genera showed considerable variation based on the patients' disease severity and cultivation in the SRB medium. In detail, samples without cultivation from patients with moderate UC showed a high abundance of the genera Bacteroides, Bifidobacterium and Ruminococcus, but after SRB cultivation, the dominant genera were Bacteroides, Klebsiella and Bilophila. On the other hand, before SRB cultivation, the main represented genera in patients with severe UC were Escherichia-Shigella, Proteus, Methanothermobacter and Methanobacterium. However, after incubation in the SRB medium Bacteroides, Proteus, Alistipes and Lachnoclostridium were predominant. Information regarding GM compositional changes in UC patients may aid the development of novel therapeutic strategies (e.g., probiotic preparations containing specific bacterial strains) to counteract the mechanisms of virulence of harmful bacteria and the subsequent inflammatory response that is closely related to the pathogenesis of inflammatory bowel diseases.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Kristýna Martínková
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Lenka Mráková
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Francesco Giudici
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Simone Baldi
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - David Novak
- Department of Biochemistry, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Márió Gajdács
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, 6720 Szeged, Hungary
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Dani Dordevic
- Department of Plant Origin Food Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Simon K.-M. R. Rittmann
- Department of Functional and Evolutionary Ecology, Archaea Physiology & Biotechnology Group, Universität Wien, 1030 Wien, Austria
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Candeliere F, Sola L, Raimondi S, Rossi M, Amaretti A. Good and bad dispositions between archaea and bacteria in the human gut: New insights from metagenomic survey and co-occurrence analysis. Synth Syst Biotechnol 2024; 9:88-98. [PMID: 38292760 PMCID: PMC10824687 DOI: 10.1016/j.synbio.2023.12.007] [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: 06/28/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024] Open
Abstract
Archaea are an understudied component of the human microbiome. In this study, the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing. Archaea were ubiquitously found in a wide range of abundances, reaching up to 7.2 %. The dominant archaeal phylum was Methanobacteriota, specifically the family Methanobacteriaceae, encompassing more than 50 % of Archaea in 50 samples. The previously underestimated Thermoplasmatota, mostly composed of Methanomassiliicoccaceae, dominated in 10 subjects (>50 %) and was present in all others except one. Halobacteriota, the sole other archaeal phylum, occurred in negligible concentration, except for two samples (4.6-4.8 %). This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway: i) hydrogenotrophic reduction of CO2 is the predominant, being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples; ii) the second pathway, that involved Methanomassiliicoccales, was the hydrogenotrophic reduction of methyl-compounds; iii) dismutation of acetate or methyl-compounds seemed to be absent. Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community, allowing to depict a clearer picture of the human gut archaeome.
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Affiliation(s)
- Francesco Candeliere
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Laura Sola
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Biogest-Siteia, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Biogest-Siteia, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Biogest-Siteia, University of Modena and Reggio Emilia, 41125 Modena, Italy
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13
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von Hoyningen-Huene AJE, Bang C, Rausch P, Rühlemann M, Fokt H, He J, Jensen N, Knop M, Petersen C, Schmittmann L, Zimmer T, Baines JF, Bosch TCG, Hentschel U, Reusch TBH, Roeder T, Franke A, Schulenburg H, Stukenbrock E, Schmitz RA. The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions. Front Microbiol 2024; 15:1347422. [PMID: 38476944 PMCID: PMC10927989 DOI: 10.3389/fmicb.2024.1347422] [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: 11/30/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.
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Affiliation(s)
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Hannover Medical School, Institute for Medical Microbiology and Hospital Epidemiology, Hannover, Germany
| | - Hanna Fokt
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jinru He
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Nadin Jensen
- Institute for General Microbiology, Kiel University, Kiel, Germany
| | - Mirjam Knop
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
| | - Carola Petersen
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lara Schmittmann
- Research Unit Ocean Dynamics, GEOMAR Helmholtz Institute for Ocean Research Kiel, Kiel, Germany
| | - Thorsten Zimmer
- Institute for General Microbiology, Kiel University, Kiel, Germany
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thomas C. G. Bosch
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ute Hentschel
- Marine Evolutionary Ecology, GEOMAR Helmholtz Center for Ocean Research, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thorsten B. H. Reusch
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thomas Roeder
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva Stukenbrock
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Kiel University, Kiel, Germany
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14
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Spohr P, Scharf S, Rommerskirchen A, Henrich B, Jäger P, Klau GW, Haas R, Dilthey A, Pfeffer K. Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing. Sci Rep 2024; 14:4068. [PMID: 38374282 PMCID: PMC10876974 DOI: 10.1038/s41598-024-53506-1] [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: 08/23/2023] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics.
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Affiliation(s)
- Philipp Spohr
- Chair Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Digital Medicine, Düsseldorf, Germany
| | - Sebastian Scharf
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Anna Rommerskirchen
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Paul Jäger
- Department of Hematology, Immunology, and Clinical Immunology, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Gunnar W Klau
- Chair Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Center for Digital Medicine, Düsseldorf, Germany.
| | - Rainer Haas
- Department of Hematology, Immunology, and Clinical Immunology, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany.
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany.
- Center for Digital Medicine, Düsseldorf, Germany.
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany.
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15
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Cisek AA, Szymańska E, Aleksandrzak-Piekarczyk T, Cukrowska B. The Role of Methanogenic Archaea in Inflammatory Bowel Disease-A Review. J Pers Med 2024; 14:196. [PMID: 38392629 PMCID: PMC10890621 DOI: 10.3390/jpm14020196] [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: 12/31/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Methanogenic archaea are a part of the commensal gut microbiota responsible for hydrogen sink and the efficient production of short-chain fatty acids. Dysbiosis of methanogens is suspected to play a role in pathogenesis of variety of diseases, including inflammatory bowel disease (IBD). Unlike bacteria, the diversity of archaea seems to be higher in IBD patients compared to healthy subjects, whereas the prevalence and abundance of gut methanogens declines in IBD, especially in ulcerative colitis. To date, studies focusing on methanogens in pediatric IBD are very limited; nevertheless, the preliminary results provide some evidence that methanogens may be influenced by the chronic inflammatory process in IBD. In this review, we demonstrated the development and diversity of the methanogenic community in IBD, both in adults and children.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathomorphology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Edyta Szymańska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | | | - Bożena Cukrowska
- Department of Pathomorphology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
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16
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McDonald AG, Lisacek F. Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens. Sci Rep 2024; 14:1649. [PMID: 38238389 PMCID: PMC10796942 DOI: 10.1038/s41598-023-51012-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/29/2023] [Indexed: 01/22/2024] Open
Abstract
The development of a stable human gut microbiota occurs within the first year of life. Many open questions remain about how microfloral species are influenced by the composition of milk, in particular its content of human milk oligosaccharides (HMOs). The objective is to investigate the effect of the human HMO glycome on bacterial symbiosis and competition, based on the glycoside hydrolase (GH) enzyme activities known to be present in microbial species. We extracted from UniProt a list of all bacterial species catalysing glycoside hydrolase activities (EC 3.2.1.-), cross-referencing with the BRENDA database, and obtained a set of taxonomic lineages and CAZy family data. A set of 13 documented enzyme activities was selected and modelled within an enzyme simulator according to a method described previously in the context of biosynthesis. A diverse population of experimentally observed HMOs was fed to the simulator, and the enzymes matching specific bacterial species were recorded, based on their appearance of individual enzymes in the UniProt dataset. Pairs of bacterial species were identified that possessed complementary enzyme profiles enabling the digestion of the HMO glycome, from which potential symbioses could be inferred. Conversely, bacterial species having similar GH enzyme profiles were considered likely to be in competition for the same set of dietary HMOs within the gut of the newborn. We generated a set of putative biodegradative networks from the simulator output, which provides a visualisation of the ability of organisms to digest HMO and mucin-type O-glycans. B. bifidum, B. longum and C. perfringens species were predicted to have the most diverse GH activity and therefore to excel in their ability to digest these substrates. The expected cooperative role of Bifidobacteriales contrasts with the surprising capacities of the pathogen. These findings indicate that potential pathogens may associate in human gut based on their shared glycoside hydrolase digestive apparatus, and which, in the event of colonisation, might result in dysbiosis. The methods described can readily be adapted to other enzyme categories and species as well as being easily fine-tuneable if new degrading enzymes are identified and require inclusion in the model.
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Affiliation(s)
- Andrew G McDonald
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland.
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland.
- Computer Science Department, University of Geneva, Geneva, Switzerland.
- Section of Biology, University of Geneva, Geneva, Switzerland.
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17
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Guerra A. Human associated Archaea: a neglected microbiome worth investigating. World J Microbiol Biotechnol 2024; 40:60. [PMID: 38172371 DOI: 10.1007/s11274-023-03842-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.
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18
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Novikova PV, Bhanu Busi S, Probst AJ, May P, Wilmes P. Functional prediction of proteins from the human gut archaeome. ISME COMMUNICATIONS 2024; 4:ycad014. [PMID: 38486809 PMCID: PMC10939349 DOI: 10.1093/ismeco/ycad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 03/17/2024]
Abstract
The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.
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Affiliation(s)
- Polina V Novikova
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- UK Centre for Ecology and Hydrology, Wallingford, OX10 8 BB, United Kingdom
| | - Alexander J Probst
- Environmental Metagenomics, Department of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, for Environmental Microbiology and Biotechnology, University Duisburg-Essen, Duisburg 47057, Germany
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Paul Wilmes
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
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19
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Orgler E, Baumgartner M, Duller S, Kumptisch C, Hausmann B, Moser D, Khare V, Lang M, Köcher T, Frick A, Muttenthaler M, Makristathis A, Moissl-Eichinger C, Gasche C. Archaea influence composition of endoscopically visible ileocolonic biofilms. Gut Microbes 2024; 16:2359500. [PMID: 38825783 PMCID: PMC11152093 DOI: 10.1080/19490976.2024.2359500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 05/21/2024] [Indexed: 06/04/2024] Open
Abstract
The gut microbiota has been implicated as a driver of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Recently we described, mucosal biofilms, signifying alterations in microbiota composition and bile acid (BA) metabolism in IBS and ulcerative colitis (UC). Luminal oxygen concentration is a key factor in the gastrointestinal (GI) ecosystem and might be increased in IBS and UC. Here we analyzed the role of archaea as a marker for hypoxia in mucosal biofilms and GI homeostasis. The effects of archaea on microbiome composition and metabolites were analyzed via amplicon sequencing and untargeted metabolomics in 154 stool samples of IBS-, UC-patients and controls. Mucosal biofilms were collected in a subset of patients and examined for their bacterial, fungal and archaeal composition. Absence of archaea, specifically Methanobrevibacter, correlated with disrupted GI homeostasis including decreased microbial diversity, overgrowth of facultative anaerobes and conjugated secondary BA. IBS-D/-M was associated with absence of archaea. Presence of Methanobrevibacter correlated with Oscillospiraceae and epithelial short chain fatty acid metabolism and decreased levels of Ruminococcus gnavus. Absence of fecal Methanobrevibacter may indicate a less hypoxic GI environment, reduced fatty acid oxidation, overgrowth of facultative anaerobes and disrupted BA deconjugation. Archaea and Ruminococcus gnavus could distinguish distinct subtypes of mucosal biofilms. Further research on the connection between archaea, mucosal biofilms and small intestinal bacterial overgrowth should be performed.
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Affiliation(s)
- Elisabeth Orgler
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Department of Medicine II, University Hospital, Munich, Germany
| | - Maximilian Baumgartner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Stefanie Duller
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christina Kumptisch
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Bela Hausmann
- Centre for Microbiology and Environmental Systems Science, Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Doris Moser
- Department of Cranio-Maxillofacial and Oral Surgery, Medical University of Vienna, Vienna, Austria
| | - Vineeta Khare
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Michaela Lang
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Thomas Köcher
- Metabolomics Service and Research Facility, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Adrian Frick
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Athanasios Makristathis
- Centre for Microbiology and Environmental Systems Science, Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christoph Gasche
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
- Loha for Life, Center for Gastroenterology and Iron Deficiency, Vienna, Austria
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20
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Palumbieri MD, Merigliano C, González-Acosta D, Kuster D, Krietsch J, Stoy H, von Känel T, Ulferts S, Welter B, Frey J, Doerdelmann C, Sanchi A, Grosse R, Chiolo I, Lopes M. Nuclear actin polymerization rapidly mediates replication fork remodeling upon stress by limiting PrimPol activity. Nat Commun 2023; 14:7819. [PMID: 38016948 PMCID: PMC10684888 DOI: 10.1038/s41467-023-43183-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/30/2023] Open
Abstract
Cells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase and observed their rapid extension in number and length upon genotoxic treatments, frequently taking contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork remodeling is linked to deregulated chromatin loading of PrimPol, which promotes unrestrained and discontinuous DNA synthesis and limits the recruitment of RAD51 and SMARCAL1 to nascent DNA. Moreover, defective nuclear actin polymerization upon mild replication interference induces chromosomal instability in a PRIMPOL-dependent manner. Hence, by limiting PrimPol activity, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.
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Affiliation(s)
| | - Chiara Merigliano
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | | | - Danina Kuster
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Department of Cellular and Molecular Medicine, Copenhagen University, Copenhagen, Denmark
| | - Thomas von Känel
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Svenja Ulferts
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Bettina Welter
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Joël Frey
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Cyril Doerdelmann
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Robert Grosse
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
- CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA.
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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21
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Borrel G, Fadhlaoui K, Ben Hania W, Gaci N, Pehau-Arnaudet G, Chaudhary PP, Vandekerckove P, Ballet N, Alric M, O’Toole PW, Fardeau ML, Ollivier B, Brugère JF. Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov. Microorganisms 2023; 11:2794. [PMID: 38004804 PMCID: PMC10673518 DOI: 10.3390/microorganisms11112794] [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: 10/28/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05T were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L-1 NaCl (optimum 0.12 mol.L-1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05T (JCM 31474T).
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Affiliation(s)
- Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell, 75015 Paris, France
| | - Khaled Fadhlaoui
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS, UMR 6023 CNRS-UCA, Laboratoire Microorganismes: Génome et Environnement LMGE, 63000 Clermont-Ferrand, France
| | - Wajdi Ben Hania
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Nadia Gaci
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Gérard Pehau-Arnaudet
- Institut Pasteur, Université Paris Cité, Ultrastructural Bioimaging, 75015 Paris, France
| | - Prem Prashant Chaudhary
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Nathalie Ballet
- Lesaffre International, Lesaffre Group, 59700 Marcq-en-Barœul, France
| | - Monique Alric
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | | | - Marie-Laure Fardeau
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
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22
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Medvedeva S, Borrel G, Krupovic M, Gribaldo S. A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment. Nat Microbiol 2023; 8:2170-2182. [PMID: 37749252 DOI: 10.1038/s41564-023-01485-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023]
Abstract
Methanogenic archaea are major producers of methane, a potent greenhouse gas and biofuel, and are widespread in diverse environments, including the animal gut. The ecophysiology of methanogens is likely impacted by viruses, which remain, however, largely uncharacterized. Here we carried out a global investigation of viruses associated with all current diversity of methanogens by assembling an extensive CRISPR database consisting of 156,000 spacers. We report 282 high-quality (pro)viral and 205 virus-like/plasmid sequences assigned to hosts belonging to ten main orders of methanogenic archaea. Viruses of methanogens can be classified into 87 families, underscoring a still largely undiscovered genetic diversity. Viruses infecting gut-associated archaea provide evidence of convergence in adaptation with viruses infecting gut-associated bacteria. These viruses contain a large repertoire of lysin proteins that cleave archaeal pseudomurein and are enriched in glycan-binding domains (Ig-like/Flg_new) and diversity-generating retroelements. The characterization of this vast repertoire of viruses paves the way towards a better understanding of their role in regulating methanogen communities globally, as well as the development of much-needed genetic tools.
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Affiliation(s)
- Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Unit Archaeal Virology, Paris, France.
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
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23
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Arenas-Gómez CM, Garcia-Gutierrez E, Escobar JS, Cotter PD. Human gut homeostasis and regeneration: the role of the gut microbiota and its metabolites. Crit Rev Microbiol 2023; 49:764-785. [PMID: 36369718 DOI: 10.1080/1040841x.2022.2142088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 08/18/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
The healthy human gut is a balanced ecosystem where host cells and representatives of the gut microbiota interact and communicate in a bidirectional manner at the gut epithelium. As a result of these interactions, many local and systemic processes necessary for host functionality, and ultimately health, take place. Impairment of the integrity of the gut epithelium diminishes its ability to act as an effective gut barrier, can contribute to conditions associated to inflammation processes and can have other negative consequences. Pathogens and pathobionts have been linked with damage of the integrity of the gut epithelium, but other components of the gut microbiota and some of their metabolites can contribute to its repair and regeneration. Here, we review what is known about the effect of bacterial metabolites on the gut epithelium and, more specifically, on the regulation of repair by intestinal stem cells and the regulation of the immune system in the gut. Additionally, we explore the potential therapeutic use of targeted modulation of the gut microbiota to maintain and improve gut homeostasis as a mean to improve health outcomes.
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Affiliation(s)
- Claudia Marcela Arenas-Gómez
- Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
- Dirección Académica, Universidad Nacional de Colombia, Sede de La Paz, La Paz 202017, Colombia
| | - Enriqueta Garcia-Gutierrez
- Teagasc Food Research Centre Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Moorepark, Fermoy, Ireland
| | - Juan S Escobar
- Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Paul D Cotter
- Teagasc Food Research Centre Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Moorepark, Fermoy, Ireland
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24
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Ou Y, Belzer C, Smidt H, de Weerth C. Methodological recommendations for human microbiota-gut-brain axis research. MICROBIOME RESEARCH REPORTS 2023; 3:1. [PMID: 38455088 PMCID: PMC10917620 DOI: 10.20517/mrr.2023.33] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 03/09/2024]
Abstract
Observational studies have determined numerous correlations between sequence-based gut microbiota data and human mental traits. However, these associations are often inconsistent across studies. This inconsistency is one of the reasons that mechanistic validation studies of the observed correlations are lagging, making it difficult to establish causal associations. The absence of consistent study findings may partially be due to the lack of clear guidelines for identifying confounders of relations between complex microbial communities and mental conditions. Gut microbial complexity also impedes deciphering microbiota-host relations by using a single analytical approach. The aim of the current review is to help solve these problems by providing methodological recommendations for future human microbiota-gut-brain axis research on the selection of confounders, the use of integrative biostatistical methods, and the steps needed to translate correlative findings into causal conclusions.
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Affiliation(s)
- Yangwenshan Ou
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH Wageningen, The Netherlands
- Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH Wageningen, The Netherlands
| | - Carolina de Weerth
- Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
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25
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Yang J, Chen R, Peng Y, Chai J, Li Y, Deng F. The role of gut archaea in the pig gut microbiome: a mini-review. Front Microbiol 2023; 14:1284603. [PMID: 37876779 PMCID: PMC10593451 DOI: 10.3389/fmicb.2023.1284603] [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: 08/28/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The gastrointestinal microbiota of swine harbors an essential but often overlooked component: the gut archaea. These enigmatic microorganisms play pivotal roles in swine growth, health, and yield quality. Recent insights indicate that the diversity of gut archaea is influenced by various factors including breed, age, and diet. Such factors orchestrate the metabolic interactions within the porcine gastrointestinal environment. Through symbiotic relationships with bacteria, these archaea modulate the host's energy metabolism and digestive processes. Contemporary research elucidates a strong association between the abundance of these archaea and economically significant traits in swine. This review elucidates the multifaceted roles of gut archaea in swine and underscores the imperative for strategic interventions to modulate their population and functionality. By exploring the probiotic potential of gut archaea, we envisage novel avenues to enhance swine growth, health, and product excellence. By spotlighting this crucial, yet under-investigated, facet of the swine gut microbiome, we aim to galvanize further scientific exploration into harnessing their myriad benefits.
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Affiliation(s)
- Jianbo Yang
- 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, Guangdong, China
| | - Routing Chen
- 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, Guangdong, 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, Guangdong, China
| | - Jianmin Chai
- 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, Guangdong, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, China
| | - 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, Guangdong, China
| | - 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, Guangdong, China
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26
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Leroux N, Sylvain FE, Holland A, Luis Val A, Derome N. Gut microbiota of an Amazonian fish in a heterogeneous riverscape: integrating genotype, environment, and parasitic infections. Microbiol Spectr 2023; 11:e0275522. [PMID: 37724869 PMCID: PMC10581195 DOI: 10.1128/spectrum.02755-22] [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: 07/20/2022] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
A number of key factors can structure the gut microbiota of fish such as environment, diet, health state, and genotype. Mesonauta festivus, an Amazonian cichlid, is a relevant model organism to study the relative contribution of these factors on the community structure of fish gut microbiota. M. festivus has well-studied genetic populations and thrives in rivers with drastically divergent physicochemical characteristics. Here, we collected 167 fish from 12 study sites and used 16S and 18S rRNA metabarcoding approaches to characterize the gut microbiome structure of M. festivus. These data sets were analyzed in light of the host fish genotypes (genotyping-by-sequencing) and an extensive characterization of environmental physico-chemical parameters. We explored the relative contribution of environmental dissimilarity, the presence of parasitic taxa, and phylogenetic relatedness on structuring the gut microbiota. We documented occurrences of Nyctotherus sp. infecting a fish and linked its presence to a dysbiosis of the host gut microbiota. Moreover, we detected the presence of helminths which had a minor impact on the gut microbiota of their host. In addition, our results support a higher impact of the phylogenetic relatedness between fish rather than environmental similarity between sites of study on structuring the gut microbiota for this Amazonian cichlid. Our study in a heterogeneous riverscape integrates a wide range of factors known to structure fish gut microbiomes. It significantly improves understanding of the complex relationship between fish, their parasites, their microbiota, and the environment. IMPORTANCE The gut microbiota is known to play important roles in its host immunity, metabolism, and comportment. Its taxonomic composition is modulated by a complex interplay of factors that are hard to study simultaneously in natural systems. Mesonauta festivus, an Amazonian cichlid, is an interesting model to simultaneously study the influence of multiple variables on the gut microbiota. In this study, we explored the relative contribution of the environmental conditions, the presence of parasitic infections, and the genotype of the host on structuring the gut microbiota of M. festivus in Amazonia. Our results highlighted infections by a parasitic ciliate that caused a disruption of the gut microbiota and by parasitic worms that had a low impact on the microbiota. Finally, our results support a higher impact of the genotype than the environment on structuring the microbiota for this fish. These findings significantly improve understanding of the complex relationship among fish, their parasites, their microbiota, and the environment.
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Affiliation(s)
- Nicolas Leroux
- Department of Biology, Laval University, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes, Quebec City, Quebec, Canada
| | - Francois-Etienne Sylvain
- Department of Biology, Laval University, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes, Quebec City, Quebec, Canada
| | - Aleicia Holland
- Department of Environment and Genetics, Centre for Freshwater Ecosystems, Wodonga, Victoria, Australia
| | - Adalberto Luis Val
- Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon, Manaus, Brazil
| | - Nicolas Derome
- Department of Biology, Laval University, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes, Quebec City, Quebec, Canada
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27
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Abstract
Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Cindy J Castelle
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
| | - Jillian F Banfield
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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28
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Abstract
Microbial communities are shaped by positive and negative interactions ranging from competition to mutualism. In the context of the mammalian gut and its microbial inhabitants, the integrated output of the community has important impacts on host health. Cross-feeding, the sharing of metabolites between different microbes, has emergent roles in establishing communities of gut commensals that are stable, resistant to invasion, and resilient to external perturbation. In this review, we first explore the ecological and evolutionary implications of cross-feeding as a cooperative interaction. We then survey mechanisms of cross-feeding across trophic levels, from primary fermenters to H2 consumers that scavenge the final metabolic outputs of the trophic network. We extend this analysis to also include amino acid, vitamin, and cofactor cross-feeding. Throughout, we highlight evidence for the impact of these interactions on each species' fitness as well as host health. Understanding cross-feeding illuminates an important aspect of microbe-microbe and host-microbe interactions that establishes and shapes our gut communities.
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Affiliation(s)
- Elizabeth J Culp
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.
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29
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Yao Q, Yu Z, Meng Q, Chen J, Liu Y, Song W, Ren X, Zhou J, Chen X. The Role of Small Intestinal Bacterial Overgrowth in Obesity and Its Related Diseases. Biochem Pharmacol 2023; 212:115546. [PMID: 37044299 DOI: 10.1016/j.bcp.2023.115546] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023]
Abstract
Obesity has become a major public health problem worldwide and its occurrence is increasing globally. Obesity has also been shown to be involved in the occurrence and development of many diseases and pathological conditions, such as nonalcoholic fatty liver disease (NAFLD), type 2 diabetes mellitus (T2DM), insulin resistance (IR). In recent years, gut microbiota has received extensive attention as an important regulatory part involved in host diseases and health status. A growing body of evidence suggests that gut microbiota dysbiosis has a significant adverse effect on the host. Small intestinal bacterial overgrowth (SIBO), a type of intestinal microbial dysbiosis, has been gradually revealed to be associated with obesity and its related diseases. The presence of SIBO may lead to the destruction of intestinal barrier integrity, increased intestinal permeability, increased endotoxin levels, activation of inflammatory responses, and translocation of bacteria from the colon to the small intestine. However, the causal relationship between SIBO and obesity and the specific mechanisms have not been well elucidated. This review discusses the cross-talk between SIBO and obesity and its related diseases, and expounds its potential mechanisms and interventions, which may help to discover new therapeutic targets for obesity and its related diseases and develop treatment options.
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Affiliation(s)
- Qinyan Yao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Zihan Yu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Qingguo Meng
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Jihua Chen
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Yaxin Liu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Wenxuan Song
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Xiangfeng Ren
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Jinjie Zhou
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Xin Chen
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China.
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30
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Bonvegna S, Cilia R. Disease mechanisms as subtypes: Microbiome. HANDBOOK OF CLINICAL NEUROLOGY 2023; 193:107-131. [PMID: 36803806 DOI: 10.1016/b978-0-323-85555-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Abnormalities in gut microbiota have been suggested to be involved in the pathophysiology and progression of Parkinson's disease (PD). Gastrointestinal nonmotor symptoms often precede the onset of motor features in PD, suggesting a role for gut dysbiosis in neuroinflammation and α-synuclein (α-syn) aggregation. In the first part of this chapter, we analyze critical features of healthy gut microbiota and factors (environmental and genetic) that modify its composition. In the second part, we focus on the mechanisms underlying the gut dysbiosis and how it alters anatomically and functionally the mucosal barrier, triggering neuroinflammation and subsequently α-syn aggregation. In the third part, we describe the most common alterations in the gut microbiota of PD patients, dividing the gastrointestinal system in higher and lower tract to examine the association between microbiota abnormalities and clinical features. In the final section, we report on current and future therapeutic approaches to gut dysbiosis aiming to either reduce the risk for PD, modify the disease course, or improve the pharmacokinetic profile of dopaminergic therapies. We also suggest that further studies will be needed to clarify the role of the microbiome in PD subtyping and of pharmacological and nonpharmacological interventions in modifying specific microbiota profiles in individualizing disease-modifying treatments in PD.
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Affiliation(s)
- Salvatore Bonvegna
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Milan, Italy
| | - Roberto Cilia
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Milan, Italy.
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31
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Kakagianni M, Tsiknia M, Feka M, Vasileiadis S, Leontidou K, Kavroulakis N, Karamanoli K, Karpouzas DG, Ehaliotis C, Papadopoulou KK. Above- and below-ground microbiome in the annual developmental cycle of two olive tree varieties. FEMS MICROBES 2023; 4:xtad001. [PMID: 37333440 PMCID: PMC10117799 DOI: 10.1093/femsmc/xtad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/18/2022] [Accepted: 01/05/2023] [Indexed: 10/22/2023] Open
Abstract
The olive tree is a hallmark crop in the Mediterranean region. Its cultivation is characterized by an enormous variability in existing genotypes and geographical areas. As regards the associated microbial communities of the olive tree, despite progress, we still lack comprehensive knowledge in the description of these key determinants of plant health and productivity. Here, we determined the prokaryotic, fungal and arbuscular mycorrhizal fungal (AMF) microbiome in below- (rhizospheric soil, roots) and above-ground (phyllosphere and carposphere) plant compartments of two olive varieties 'Koroneiki' and 'Chondrolia Chalkidikis' grown in Southern and Northern Greece respectively, in five developmental stages along a full fruit-bearing season. Distinct microbial communities were supported in above- and below-ground plant parts; while the former tended to be similar between the two varieties/locations, the latter were location specific. In both varieties/locations, a seasonally stable root microbiome was observed over time; in contrast the plant microbiome in the other compartments were prone to changes over time, which may be related to seasonal environmental change and/or to plant developmental stage. We noted that olive roots exhibited an AMF-specific filtering effect (not observed for bacteria and general fungi) onto the rhizosphere AMF communities of the two olive varieties/locations/, leading to the assemblage of homogenous intraradical AMF communities. Finally, shared microbiome members between the two olive varieties/locations include bacterial and fungal taxa with putative functional attributes that may contribute to olive tree tolerance to abiotic and biotic stress.
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Affiliation(s)
- Myrsini Kakagianni
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa 41500, Greece
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Thessaly, Temponera str, 43100 Karditsa, Greece
| | - Myrto Tsiknia
- Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Athens 11855, Greece
| | - Maria Feka
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa 41500, Greece
| | - Sotirios Vasileiadis
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa 41500, Greece
| | - Kleopatra Leontidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Nektarios Kavroulakis
- Institute for Olive Tree, Subtropical Plants and Viticulture, Hellenic Agricultural Organization “ELGO-Dimitra”, Agrokipio-Souda, 73164 Chania, Greece
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Dimitrios G Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa 41500, Greece
| | - Constantinos Ehaliotis
- Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Athens 11855, Greece
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa 41500, Greece
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32
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Liu X, He G, Lan Y, Guo W, Liu X, Li J, Liu A, He M, Liu X, Fan Z, Zhang Y. Virome and metagenomic analysis reveal the distinct distribution of microbiota in human fetal gut during gestation. Front Immunol 2023; 13:1079294. [PMID: 36685560 PMCID: PMC9850102 DOI: 10.3389/fimmu.2022.1079294] [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: 10/25/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023] Open
Abstract
Studies have shown that fetal immune cell activation may result from potential exposure to microbes, although the presence of microbes in fetus has been a controversial topic. Here, we combined metagenomic and virome techniques to investigate the presence of bacteria and viruses in fetal tissues (small intestine, cecum, and rectum). We found that the fetal gut is not a sterile environment and has a low abundance but metabolically rich microbiome. Specifically, Proteobacteria and Actinobacteria were the dominant bacteria phyla of fetal gut. In total, 700 species viruses were detected, and Human betaherpesvirus 5 was the most abundant eukaryotic viruses. Especially, we first identified Methanobrevibacter smithii in fetal gut. Through the comparison with adults' gut microbiota we found that Firmicutes and Bacteroidetes gradually became the main force of gut microbiota during the process of growth and development. Interestingly, 6 antibiotic resistance genes were shared by the fetus and adults. Our results indicate the presence of microbes in the fetal gut and demonstrate the diversity of bacteria, archaea and viruses, which provide support for the studies related to early fetal immunity. This study further explores the specific composition of viruses in the fetal gut and the similarities between fetal and adults' gut microbiota, which is valuable for understanding human fetal immunity development during gestation.
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Affiliation(s)
- Xu Liu
- Key Laboratory of Bioresources and Ecoenvironment, Ministry of Education, College of Life Sciences, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guolin He
- Key Laboratory of Bioresources and Ecoenvironment, Ministry of Education, College of Life Sciences, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China,Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yue Lan
- Key Laboratory of Bioresources and Ecoenvironment, Ministry of Education, College of Life Sciences, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Weijie Guo
- Key Laboratory of Bioresources and Ecoenvironment, Ministry of Education, College of Life Sciences, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xuyuan Liu
- Key Laboratory of Bioresources and Ecoenvironment, Ministry of Education, College of Life Sciences, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment, Ministry of Education, College of Life Sciences, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Anqing Liu
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan, China
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan, China
| | - Xinhui Liu
- Key Laboratory of Bioresources and Ecoenvironment, Ministry of Education, College of Life Sciences, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China,Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment, Ministry of Education, College of Life Sciences, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China,*Correspondence: Yaoyao Zhang, ; Zhenxin Fan,
| | - Yaoyao Zhang
- Key Laboratory of Bioresources and Ecoenvironment, Ministry of Education, College of Life Sciences, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China,Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China,*Correspondence: Yaoyao Zhang, ; Zhenxin Fan,
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Ali RO, Quinn GM, Umarova R, Haddad JA, Zhang GY, Townsend EC, Scheuing L, Hill KL, Gewirtz M, Rampertaap S, Rosenzweig SD, Remaley AT, Han JM, Periwal V, Cai H, Walter PJ, Koh C, Levy EB, Kleiner DE, Etzion O, Heller T. Longitudinal multi-omics analyses of the gut-liver axis reveals metabolic dysregulation in hepatitis C infection and cirrhosis. Nat Microbiol 2023; 8:12-27. [PMID: 36522461 DOI: 10.1038/s41564-022-01273-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/18/2022] [Indexed: 12/23/2022]
Abstract
The gut and liver are connected via the portal vein, and this relationship, which includes the gut microbiome, is described as the gut-liver axis. Hepatitis C virus (HCV) can infect the liver and cause fibrosis with chronic infection. HCV has been associated with an altered gut microbiome; however, how these changes impact metabolism across the gut-liver axis and how this varies with disease severity and time is unclear. Here we used multi-omics analysis of portal and peripheral blood, faeces and liver tissue to characterize the gut-liver axis of patients with HCV across a fibrosis severity gradient before (n = 29) and 6 months after (n = 23) sustained virologic response, that is, no detection of the virus. Fatty acids were the major metabolites perturbed across the liver, portal vein and gut microbiome in HCV, especially in patients with cirrhosis. Decreased fatty acid degradation by hepatic peroxisomes and mitochondria was coupled with increased free fatty acid (FFA) influx to the liver via the portal vein. Metatranscriptomics indicated that Anaerostipes hadrus-mediated fatty acid synthesis influences portal FFAs. Both microbial fatty acid synthesis and portal FFAs were associated with enhanced hepatic fibrosis. Bacteroides vulgatus-mediated intestinal glycan breakdown was linked to portal glycan products, which in turn correlated with enhanced portal inflammation in HCV. Paired comparison of patient samples at both timepoints showed that hepatic metabolism, especially in peroxisomes, is persistently dysregulated in cirrhosis independently of the virus. Sustained virologic response was associated with a potential beneficial role for Methanobrevibacter smithii, which correlated with liver disease severity markers. These results develop our understanding of the gut-liver axis in HCV and non-HCV liver disease aetiologies and provide a foundation for future therapies.
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Affiliation(s)
- Rabab O Ali
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Gabriella M Quinn
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Regina Umarova
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James A Haddad
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Grace Y Zhang
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth C Townsend
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lisa Scheuing
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kareen L Hill
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Meital Gewirtz
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shakuntala Rampertaap
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Alan T Remaley
- Cardiovascular and Pulmonary Branch of the National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jung Min Han
- Computational Medicine Section, Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vipul Periwal
- Computational Medicine Section, Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hongyi Cai
- Clinical Mass Spectrometry Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter J Walter
- Clinical Mass Spectrometry Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Koh
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elliot B Levy
- Center for Interventional Oncology, Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - David E Kleiner
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ohad Etzion
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Theo Heller
- Translational Hepatology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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Jiang H, Deng S, Zhang J, Chen J, Li B, Zhu W, Zhang M, Zhang C, Meng Z. Acupuncture treatment for post-stroke depression: Intestinal microbiota and its role. Front Neurosci 2023; 17:1146946. [PMID: 37025378 PMCID: PMC10070763 DOI: 10.3389/fnins.2023.1146946] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
Stroke-induced depression is a common complication and an important risk factor for disability. Besides psychiatric symptoms, depressed patients may also exhibit a variety of gastrointestinal symptoms, and even take gastrointestinal symptoms as the primary reason for medical treatment. It is well documented that stress may disrupt the balance of the gut microbiome in patients suffering from post-stroke depression (PSD), and that disruption of the gut microbiome is closely related to the severity of the condition in depressed patients. Therefore, maintaining the balance of intestinal microbiota can be the focus of research on the mechanism of acupuncture in the treatment of PSD. Furthermore, stroke can be effectively treated with acupuncture at all stages and it may act as a special microecological regulator by regulating intestinal microbiota as well. In this article, we reviewed the studies on changing intestinal microbiota after acupuncture treatment and examined the existing problems and development prospects of acupuncture, microbiome, and poststroke depression, in order to provide new ideas for future acupuncture research.
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Affiliation(s)
- Hailun Jiang
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shizhe Deng
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jieying Zhang
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Junjie Chen
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Boxuan Li
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Weiming Zhu
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Menglong Zhang
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Chao Zhang
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Chao Zhang,
| | - Zhihong Meng
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Zhihong Meng,
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Weiland-Bräuer N, Saleh L, Schmitz RA. Functional Metagenomics as a Tool to Tap into Natural Diversity of Valuable Biotechnological Compounds. Methods Mol Biol 2023; 2555:23-49. [PMID: 36306077 DOI: 10.1007/978-1-0716-2795-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The marine ecosystem covers more than 70% of the world's surface, and oceans represent a source of varied types of organisms due to the diversified environment. Consequently, the marine environment is an exceptional depot of novel bioactive natural products, with structural and chemical features generally not found in terrestrial habitats. Here, in particular, microbes represent a vast source of unknown and probably new physiological characteristics. They have evolved during extended evolutionary processes of physiological adaptations under various environmental conditions and selection pressures. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. Thus, metagenomic tools are required to exploit the untapped marine microbial diversity and their bioactive compounds. This chapter focuses on function-based marine metagenomics to screen for bioactive molecules of value for biotechnology. Functional metagenomic strategies are described, including sampling in the marine environment, constructing marine metagenomic large-insert libraries, and examples on function-based screens for quorum quenching and anti-biofilm activities.
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Affiliation(s)
- Nancy Weiland-Bräuer
- Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany
| | - Livía Saleh
- Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany.
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36
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Santiago-Martínez MG, Ferry JG. Methods for Culturing Anaerobic Microorganisms. Methods Mol Biol 2023; 2648:231-238. [PMID: 37039994 DOI: 10.1007/978-1-0716-3080-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Anaerobic microorganisms (anaerobes) proliferate in diverse oxygen-free environments. They inhabit Earth's soils and aquatic sediments, the rumen and gut of mammals, and the gut of insects among many other oxygen-free environments. Anaerobes impact biotechnological, biomedical, ecological, and astrobiological fields. Sensitivity to oxygen is of prime consideration for successful culturing which is essential to understand function. Although cultivated for many years, the protocols and media components have been modified and adapted to the special needs of species, as well as conditions and variables for experimental evaluations. Here we describe a revised method used in our laboratories for the growth of methane-producing anaerobes (methanogenic archaea) which are among the most oxygen sensitive. The method is an example for the preparation of more specific media to cultivate a wide diversity of anaerobes.
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Affiliation(s)
- Michel Geovanni Santiago-Martínez
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
| | - James Gregory Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
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37
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Li R, Wang Y, Hu H, Tan Y, Ma Y. Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut. Nat Commun 2022; 13:7978. [PMID: 36581612 PMCID: PMC9800368 DOI: 10.1038/s41467-022-35735-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
The human gut microbiome has been extensively explored, while the archaeal viruses remain largely unknown. Here, we present a comprehensive analysis of the archaeal viruses from the human gut metagenomes and the existing virus collections using the CRISPR spacer and viral signature-based approach. This results in 1279 viral species, of which, 95.2% infect Methanobrevibacteria_A, 56.5% shared high identity (>95%) with the archaeal proviruses, 37.2% have a host range across archaeal species, and 55.7% are highly prevalent in the human population (>1%). A methanogenic archaeal virus-specific gene for pseudomurein endoisopeptidase (PeiW) frequently occurs in the viral sequences (n = 150). Analysis of 33 Caudoviricetes viruses with a complete genome often discovers the genes (integrase, n = 29; mazE, n = 10) regulating the viral lysogenic-lytic cycle, implying the dominance of temperate viruses in the archaeal virome. Together, our work uncovers the unexplored diversity of archaeal viruses, revealing the novel facet of the human gut microbiome.
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Affiliation(s)
- Ran Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongming Wang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Han Hu
- Xbiome, Scientific Research Building, Tsinghua High-Tech Park, Shenzhen, China
| | - Yan Tan
- Xbiome, Scientific Research Building, Tsinghua High-Tech Park, Shenzhen, China
| | - Yingfei Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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38
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Hoegenauer C, Hammer HF, Mahnert A, Moissl-Eichinger C. Methanogenic archaea in the human gastrointestinal tract. Nat Rev Gastroenterol Hepatol 2022; 19:805-813. [PMID: 36050385 DOI: 10.1038/s41575-022-00673-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/26/2022] [Indexed: 12/24/2022]
Abstract
The human microbiome is strongly interwoven with human health and disease. Besides bacteria, viruses and eukaryotes, numerous archaea are located in the human gastrointestinal tract and are responsible for methane production, which can be measured in clinical methane breath analyses. Methane is an important readout for various diseases, including intestinal methanogen overgrowth. Notably, the archaea responsible for methane production are largely overlooked in human microbiome studies due to their non-bacterial biology and resulting detection issues. As such, their importance for health and disease remains largely unclear to date, in particular as not a single archaeal representative has been deemed to be pathogenic. In this Perspective, we discuss the current knowledge on the clinical relevance of methanogenic archaea. We explain the archaeal unique response to antibiotics and their negative and positive effects on human physiology, and present the current understanding of the use of methane as a diagnostic marker.
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Affiliation(s)
- Christoph Hoegenauer
- Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Heinz F Hammer
- Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Department of Microbiology, Hygiene and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Department of Microbiology, Hygiene and Environmental Medicine, Medical University of Graz, Graz, Austria.
- BioTechMed Graz, Graz, Austria.
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39
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Ottmann M. [These viruses that inhabit and visit us: The human virome]. Med Sci (Paris) 2022; 38:1028-1038. [PMID: 36692282 DOI: 10.1051/medsci/2022161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recent advances in new sequencing technologies have opened the way to the deciphering of human virome. So far, human virome is defined as the complete list of viruses found in human body. Those viruses could be endogenous, prokaryotic, archaeal and eukaryotic. In addition, each compartment of the human body constitutes a different microenvironment with its own virome. Viral infections can be categorized according to the outcome of the acute phase and until recently, only symptomatic and pathological infections were studied. It is now well established that a healthy person has an extremely diverse virome. This review summarizes the current state of our knowledge and also proposes another classification of the human virome based on principles of ecology.
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Affiliation(s)
- Michèle Ottmann
- Centre international de recherche en infectiologie (CIRI), université Claude Bernard-Lyon 1, université de Lyon, Inserm U1111 - CNRS UMR 5308 - ENS, Laboratoire de virologie et pathologies humaines, Faculté de médecine RTH Laennec, 7 rue Guillaume Paradin, 69372 Lyon cedex 08, France
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40
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Zhang F, Aschenbrenner D, Yoo JY, Zuo T. The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly. THE LANCET. MICROBE 2022; 3:e969-e983. [PMID: 36182668 DOI: 10.1016/s2666-5247(22)00203-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 02/06/2023]
Abstract
The gut mycobiome (fungi) is a small but crucial component of the gut microbiome in humans. Intestinal fungi regulate host homoeostasis, pathophysiological and physiological processes, and the assembly of the co-residing gut bacterial microbiome. Over the past decade, accumulating studies have characterised the gut mycobiome in health and several pathological conditions. We review the compositional and functional diversity of the gut mycobiome in healthy populations from birth to adulthood. We describe factors influencing the gut mycobiome and the roles of intestinal fungi-especially Candida and Saccharomyces spp-in diseases and therapies with a particular focus on their synergism with the gut bacterial microbiome and host immunity. Finally, we discuss the underappreciated effects of gut fungi in clinical implications, and highlight future microbiome-based therapies that harness the tripartite relationship among the gut mycobiome, bacterial microbiome, and host immunity, aiming to restore a core gut mycobiome and microbiome and to improve clinical efficacy.
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Affiliation(s)
- Fen Zhang
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, College of Science and Engineering, Jinan University, Guangzhou, China
| | - Dominik Aschenbrenner
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma, Basel, Switzerland
| | - Ji Youn Yoo
- College of Nursing, University of Tennessee, Knoxville, TN, USA
| | - Tao Zuo
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yatsen University, Sun Yat-sen University, Guangzhou, China; Laboratory Animals Centre, Zhongshan School of Medicine, Sun Yatsen University, Guangzhou, China.
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41
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Lyu Z, Rotaru AE, Pimentel M, Zhang CJ, Rittmann SKMR. Editorial: The methane moment - Cross-boundary significance of methanogens: Preface. Front Microbiol 2022; 13:1055494. [PMID: 36504803 PMCID: PMC9731359 DOI: 10.3389/fmicb.2022.1055494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Zhe Lyu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Zhe Lyu
| | - Amelia-Elena Rotaru
- Nordic Center for Earth Evolution (NORDCEE), University of Southern Denmark, Odense, Denmark,Amelia-Elena Rotaru
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States,Mark Pimentel
| | - Cui-Jing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China,Cui-Jing Zhang
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria,Simon K.-M. R. Rittmann
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42
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Comparative Genomic Insights into Chemoreceptor Diversity and Habitat Adaptation of Archaea. Appl Environ Microbiol 2022; 88:e0157422. [DOI: 10.1128/aem.01574-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Archaea are capable of sensing and responding to environmental changes by several signal transduction systems with different mechanisms. Much attention is paid to model organisms with complex signaling networks to understand their composition and function, but general principles regarding how an archaeal species organizes its chemoreceptor diversity and habitat adaptation are poorly understood.
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43
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Luo T, Li Y, Zhang W, Liu J, Shi H. Rumen and fecal microbiota profiles associated with immunity of young and adult goats. Front Immunol 2022; 13:978402. [PMID: 36177023 PMCID: PMC9513485 DOI: 10.3389/fimmu.2022.978402] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Low immunity at birth increases risk of disease of young livestock, such as goat kids. Microbiomes change as animals mature, and a healthy microbiome is related to decreased risk of disease. The relationship between microbiota profiles and immunity at different developmental stages remains unclear. Young (female, n = 12, 30 d) and adult (female, n = 12, 2 yrs. old) Saanen dairy goats were used to investigate changes in rumen microbiomes, fecal microbiomes, and their correlations to circulating immune factors. Serum IgG (P = 0.02) and IgM (P < 0.01) were higher at 2 years than 30 d of age, but there were no differences in IgA (P = 0.34), IL-2 (P = 0.05), IL-4 (P = 0.37) and IL-6 (P = 0.73) between ages. Amplicon sequencing analysis revealed young goats had a higher diversity of bacterial communities in rumen and lower diversity in feces compared with adult goats. Ten genera in rumen and 14 genera in feces were positively correlated with serum IgM concentration across both ages. Olsenella, Methanosphaera, Quinella, Candidatus_Saccharimonas, and Methanobrevibacter in rumen and Ruminobacter, Treponema, Rikenelaceae_ RC9_ gut_ Group in feces were positively correlated with the concentration of IgG. The correlation analysis using weighted gene co-expression network analysis showed the MEblue module was positively associated with the IgG and IgM. These data provide novel insight into the association between rumen-feces microbiota and immune response. Further experiments are needed to investigate whether inoculating young livestock with immune-related bacteria identified can improve the immune status. Our data suggest a possible strategy to improve the immunity of the kids by alterative microbiota profiles.
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Affiliation(s)
- Tao Luo
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yongtao Li
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Wenying Zhang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jianxin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hengbo Shi
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- *Correspondence: Hengbo Shi,
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Bai X, Sun Y, Li Y, Li M, Cao Z, Huang Z, Zhang F, Yan P, Wang L, Luo J, Wu J, Fan D, Chen H, Zhi M, Lan P, Zeng Z, Wu X, Miao Y, Zuo T. Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population. MICROBIOME 2022; 10:147. [PMID: 36100953 PMCID: PMC9469561 DOI: 10.1186/s40168-022-01335-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/26/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND AND AIMS The human gut is home to a largely underexplored microbiome component, the archaeome. Little is known of the impact of geography, urbanization, ethnicity, and diet on the gut archaeome in association with host health. We aim to delineate the variation of the human gut archaeome in healthy individuals and its association with environmental factors and host homeostasis. METHODS Using metagenomic sequencing, we characterized the fecal archaeomes of 792 healthy adult subjects from 5 regions in China, spanning 6 ethnicities (Han, Zang, Miao, Bai, Dai, and Hani), consisting of both urban and rural residents for each ethnicity. In addition, we sampled 119 host variables (including lifestyle, diet, and blood parameters) and interrogated the influences of those factors, individually and combined, on gut archaeome variations. RESULTS Population geography had the strongest impact on the gut archaeome composition, followed by urbanization, dietary habit, and ethnicity. Overall, the metadata had a cumulative effect size of 11.0% on gut archaeome variation. Urbanization decreased both the α-diversity (intrinsic microbial diversity) and the β-diversity (inter-individual dissimilarities) of the gut archaeome, and the archaea-to-bacteria ratios in feces, whereas rural residents were enriched for Methanobrevibacter smithii in feces. Consumption of buttered milk tea (a characteristic diet of the rural Zang population) was associated with increased abundance of M. smithii. M. smithii was at the central hub of archaeal-bacterial interactions in the gut microecology, where it was positively correlated with the abundances of a multitude of short chain fatty acid (SCFA)-producing bacteria (including Roseburia faecis, Collinsella aerofaciens, and Prevotella copri). Moreover, a decreased abundance of M. smithii was associated with increased human blood levels of cholinesterase in the urban population, coinciding with the increasing prevalence of noncommunicable diseases (such as dementia) during urbanization. CONCLUSIONS Our data highlight marked contributions of environmental and host factors (geography, urbanization, ethnicity, and habitual diets) to gut archaeome variations across healthy individuals, and underscore the impact of urbanization on the gut archaeome in association with host health in modern society. Video Abstract.
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Affiliation(s)
- Xiaowu Bai
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, Yunnan, China
| | - Yue Li
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Maojuan Li
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, Yunnan, China
| | - Zhirui Cao
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ziyu Huang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Feng Zhang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ping Yan
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, Yunnan, China
| | - Lan Wang
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, Yunnan, China
| | - Juan Luo
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, Yunnan, China
| | - Jing Wu
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, Yunnan, China
| | - Dejun Fan
- Department of Gastrointestinal Endoscopy, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongxia Chen
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Min Zhi
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ping Lan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhong Zeng
- Department of Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan, China.
| | - Xiaojian Wu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, Yunnan, China.
| | - Tao Zuo
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China.
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Comparison of Changes in Gut Microbiota in Wild Boars and Domestic Pigs Using 16S rRNA Gene and Metagenomics Sequencing Technologies. Animals (Basel) 2022; 12:ani12172270. [PMID: 36077990 PMCID: PMC9454828 DOI: 10.3390/ani12172270] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/09/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The microbiota co-evolves with the host and plays an important role in the host's health, immunity, and nutrient absorption. Wild boars are the ancestors of domestic pigs. During the long evolutionary process, the physiological structure and living habits of modern pigs have undergone tremendous changes. However, there are few studies on the evolution of gut microbiota of wild boars and domestic pigs. In this study, by comparing the changes in the composition and function of the gut microbiota of wild boars and domestic pigs, it was found that there were significant differences between the two groups, which indicated that the gut microbiota had changed during the evolution process. This study provides some data references for the evolution of gut microbiota. Abstract Gut microbiota diversity is a result of co-evolution between microorganisms and their hosts. However, there are few studies on the evolution of the gut microbiota of wild boars and domestic pigs. Therefore, this study aimed to analyze the composition and function of the gut microbiota of wild boars and domestic pigs using 16S rRNA gene V3-V4 region sequencing, 16S rRNA gene full-length sequencing, and metagenomic sequencing. This study showed that after a long evolution, as compared to wild boars, the domestic pigs exhibited significantly increased relative abundances of Lactobacillus, Lactobacillus reuteri, Lactobacillus johnsonii, Lactobacillus sp.DJF_WC5, and Lactobacillus; s_uncultured bacterium, while the relative abundances of Bifidobacterium and Methanococcaceae decreased significantly. In addition, the relative abundances of “carbohydrate metabolism”, “starch and sucrose metabolism”, “valine, leucine, and isoleucine biosynthesis”, “lysine biosynthesis”, and starch-degrading CAZymes were significantly increased in the domestic pigs, while the relative abundances of “environmental adaptation”, “immune system”, “fatty acid degradation and synthesis”, and cellulose-hemicellulose-degrading CAZymes were significantly increased in the wild boars. Finally, the diversity of ARGs and the “antimicrobial resistance genes” in domestic pigs also increased significantly. This study illustrates that the gut microbiota composition and function of wild boars and domestic pigs changed during the long evolution process. These findings provide a basic research theory for the evolution of gut microbiota and the treatment of health and disease.
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Puce L, Hampton-Marcell J, Trabelsi K, Ammar A, Chtourou H, Boulares A, Marinelli L, Mori L, Cotellessa F, Currà A, Trompetto C, Bragazzi NL. Swimming and the human microbiome at the intersection of sports, clinical, and environmental sciences: A scoping review of the literature. Front Microbiol 2022; 13:984867. [PMID: 35992695 PMCID: PMC9382026 DOI: 10.3389/fmicb.2022.984867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
The human microbiota is comprised of more than 10–100 trillion microbial taxa and symbiotic cells. Two major human sites that are host to microbial communities are the gut and the skin. Physical exercise has favorable effects on the structure of human microbiota and metabolite production in sedentary subjects. Recently, the concept of “athletic microbiome” has been introduced. To the best of our knowledge, there exists no review specifically addressing the potential role of microbiomics for swimmers, since each sports discipline requires a specific set of techniques, training protocols, and interactions with the athletic infrastructure/facility. Therefore, to fill in this gap, the present scoping review was undertaken. Four studies were included, three focusing on the gut microbiome, and one addressing the skin microbiome. It was found that several exercise-related variables, such as training volume/intensity, impact the athlete’s microbiome, and specifically the non-core/peripheral microbiome, in terms of its architecture/composition, richness, and diversity. Swimming-related power-/sprint- and endurance-oriented activities, acute bouts and chronic exercise, anaerobic/aerobic energy systems have a differential impact on the athlete’s microbiome. Therefore, their microbiome can be utilized for different purposes, including talent identification, monitoring the effects of training methodologies, and devising ad hoc conditioning protocols, including dietary supplementation. Microbiomics can be exploited also for clinical purposes, assessing the effects of exposure to swimming pools and developing potential pharmacological strategies to counteract the insurgence of skin infections/inflammation, including acne. In conclusion, microbiomics appears to be a promising tool, even though current research is still limited, warranting, as such, further studies.
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Affiliation(s)
- Luca Puce
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Jarrad Hampton-Marcell
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Khaled Trabelsi
- Institut Supérieur du Sport et de l’Éducation Physique de Sfax, Université de Sfax, Sfax, Tunisia
- Research Laboratory: Education, Motricité, Sport et Santé, EM2S, Sfax University, Sfax, Tunisia
| | - Achraf Ammar
- Department of Training and Movement Science, Institute of Sport Science, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Sport Science, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Interdisciplinary Laboratory in Neurosciences, Physiology and Psychology: Physical Activity, Health and Learning (LINP2), Université Paris Lumières, Paris Nanterre University, Nanterre, France
| | - Hamdi Chtourou
- Institut Supérieur du Sport et de l’Éducation Physique de Sfax, Université de Sfax, Sfax, Tunisia
- Activité Physique, Sport et Santé, UR18JS01, Observatoire National du Sport, Tunis, Tunisia
| | - Ayoub Boulares
- Higher Institute of Sports and Physical Education of Ksar-Said, University of Manouba, Tunis, Tunisia
| | - Lucio Marinelli
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Laura Mori
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Filippo Cotellessa
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Antonio Currà
- Department of Medical-Surgical Sciences and Biotechnologies, A. Fiorini Hospital, Sapienza University of Rome, Latina, Italy
| | - Carlo Trompetto
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Nicola Luigi Bragazzi
- Laboratory for Industrial and Applied Mathematics, Department of Mathematics and Statistics, York University, Toronto, ON, Canada
- *Correspondence: Nicola Luigi Bragazzi,
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Zhang S, Ning R, Zeng B, Deng F, Kong F, Guo W, Zhao J, Li Y. Gut Microbiota Composition and Metabolic Potential of Long-Living People in China. Front Aging Neurosci 2022; 14:820108. [PMID: 35875797 PMCID: PMC9300991 DOI: 10.3389/fnagi.2022.820108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/10/2022] [Indexed: 11/15/2022] Open
Abstract
Individuals with naturally long-life spans have been extensively studied to gain a greater understanding of what factors contribute to their overall health and ability to delay or avoid certain diseases. Our previous work showed that gut microbiota can be a new avenue in healthy aging studies. In the present study, a total of 86 Chinese individuals were assigned into three groups: the long-living group (90 + years old; n = 28), the elderly group (65–75 years old; n = 31), and the young group (24–48 years old; n = 27). These groups were used to explore the composition and functional genes in the microbiota community by using the metagenomic sequencing method. We found that long-living individuals maintained high diversity in gene composition and functional profiles. Furthermore, their microbiota displays less inter-individual variation than that of elderly adults. In the taxonomic composition, it was shown that long-living people contained more short-chain fatty acid (SCFA)-producing bacteria and a decrease in certain pathogenic bacteria. Functional analysis also showed that the long-living people were enriched in metabolism metabolites methanol, trimethylamine (TMA), and CO2 to methane, and lysine biosynthesis, but the genes related to riboflavin (vitamin B2) metabolism and tryptophan biosynthesis were significantly reduced in long-living individuals. Further, we found that long-living people with enriched SCFA- and lactic-producing bacteria and related genes, highly centered on producing key lactic acid genes (ldhA) and the genes of lysine that are metabolized to the butyrate pathway. In addition, we compared the gut microbiota signatures of longevity in different regions and found that the composition of the gut microbiota of the long-lived Chinese and Italian people was quite different, but both groups were enriched in genes related to methane production and glucose metabolism. In terms of SCFA metabolism, the Chinese long-living people were enriched with bacteria and genes related to butyric acid production, while the Italian long-living people were enriched with more acetic acid-related genes. These findings suggest that the gut microbiota of Chinese long-living individuals include more SCFA-producing bacteria and genes, metabolizes methanol, TMA, and CO2, and contains fewer pathogenic bacteria, thereby potentially contributing to the healthy aging of humans.
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Affiliation(s)
- Siyuan Zhang
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Ruihong Ning
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Feilong Deng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Fanli Kong
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Wei Guo
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, 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
- *Correspondence: Ying Li,
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Madigan KE, Bundy R, Weinberg RB. Distinctive Clinical Correlates of Small Intestinal Bacterial Overgrowth with Methanogens. Clin Gastroenterol Hepatol 2022; 20:1598-1605.e2. [PMID: 34597730 DOI: 10.1016/j.cgh.2021.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Most patients with small intestinal bacterial overgrowth (SIBO) produce hydrogen by fermentation of dietary carbohydrates; however, ∼30% of patients with SIBO are colonized with Archaea, anaerobic organisms that produce methane. SIBO is associated with a plethora of symptoms and conditions, but their diagnostic significance is unclear. We aimed to determine if specific symptoms and conditions are associated with methanogenic SIBO. METHODS This study received institutional review board approval (IRB00059873). In this retrospective cross-sectional study, we queried a database of glucose breath tests conducted for suspected SIBO at our tertiary care medical center, which included data on the presence or absence of gastrointestinal symptoms and conditions often associated with SIBO. All patients had undergone a standardized breath testing protocol. RESULTS In a cohort of 1461 patients, 33.1% were SIBO positive; of these, 49.8% produced only hydrogen, 38.8% produced only methane, and 11.4% produced both gases. The following factors distinguished patients with hydrogen-producing SIBO, but not methanogenic SIBO, from SIBO-negative patients: vitamin B12 deficiency (odds ratio, 1.44; confidence interval [CI], 1.01-2.06; P = .046), Roux-en-Y gastric bypass (odds ratio, 2.14; CI, 1.09-4.18; P = .027), cholecystectomy (odds ratio, 1.42; CI, 1.06-1.91; P = .020), and diabetes (odds ratio, 1.59; CI, 1.13-2.24; P = .008). The absence of vitamin B12 deficiency was the sole discriminating factor between methanogenic and hydrogenic SIBO (odds ratio, 0.57; CI, 0.34-0.97; P = .038). CONCLUSIONS Patients with SIBO caused by methane-producing Archaea display a different spectrum of associated symptoms and clinical conditions compared with patients with SIBO caused by hydrogen-producing bacteria, particularly a lower incidence of vitamin B12 deficiency.
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Affiliation(s)
- Katelyn E Madigan
- Department of Internal Medicine, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Richa Bundy
- Department of Internal Medicine, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Richard B Weinberg
- Department of Internal Medicine-Gastroenterology, Wake Forest School of Medicine, Winston Salem, North Carolina; Department of Physiology & Pharmacology, Wake Forest School of Medicine, Winston Salem, North Carolina.
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Xiong X, Rao Y, Tu X, Wang Z, Gong J, Yang Y, Wu H, Liu X. Gut archaea associated with bacteria colonization and succession during piglet weaning transitions. BMC Vet Res 2022; 18:243. [PMID: 35751084 PMCID: PMC9229118 DOI: 10.1186/s12917-022-03330-4] [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: 03/23/2022] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods. Results We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3. Conclusion Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03330-4.
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Affiliation(s)
- Xinwei Xiong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China.
| | - Yousheng Rao
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Xutang Tu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Zhangfeng Wang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Jishang Gong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Yanbei Yang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Haobin Wu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Xianxian Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, 330006, People's Republic of China.
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Krawczyk KT, Locht C, Kowalewicz-Kulbat M. Halophilic Archaea Halorhabdus Rudnickae and Natrinema Salaciae Activate Human Dendritic Cells and Orient T Helper Cell Responses. Front Immunol 2022; 13:833635. [PMID: 35720372 PMCID: PMC9204267 DOI: 10.3389/fimmu.2022.833635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 04/28/2022] [Indexed: 12/03/2022] Open
Abstract
Halophilic archaea are procaryotic organisms distinct from bacteria, known to thrive in hypersaline environments, including salt lakes, salterns, brines and salty food. They have also been identified in the human microbiome. The biological significance of halophiles for human health has rarely been examined. The interactions between halophilic archaea and human dendritic cells (DCs) and T cells have not been identified so far. Here, we show for the first time that the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae activate human monocyte-derived DCs, induce DC maturation, cytokine production and autologous T cell activation. In vitro both strains induced DC up-regulation of the cell-surface receptors CD86, CD80 and CD83, and cytokine production, including IL-12p40, IL-10 and TNF-α, but not IL-23 and IL-12p70. Furthermore, autologous CD4+ T cells produced significantly higher amounts of IFN-γ and IL-13, but not IL-17A when co-cultured with halophile-stimulated DCs in comparison to T cells co-cultured with unstimulated DCs. IFN-γ was almost exclusively produced by naïve T cells, while IL-13 was produced by both naïve and memory CD4+ T cells. Our findings thus show that halophilic archaea are recognized by human DCs and are able to induce a balanced cytokine response. The immunomodulatory functions of halophilic archaea and their potential ability to re-establish the immune balance may perhaps participate in the beneficial effects of halotherapies.
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Affiliation(s)
- Krzysztof T Krawczyk
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Camille Locht
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Magdalena Kowalewicz-Kulbat
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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