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Rook GAW. Evolution and the critical role of the microbiota in the reduced mental and physical health associated with low socioeconomic status (SES). Neurosci Biobehav Rev 2024; 161:105653. [PMID: 38582194 DOI: 10.1016/j.neubiorev.2024.105653] [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: 11/28/2023] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The evolution of the gut-microbiota-brain axis in animals reveals that microbial inputs influence metabolism, the regulation of inflammation and the development of organs, including the brain. Inflammatory, neurodegenerative and psychiatric disorders are more prevalent in people of low socioeconomic status (SES). Many aspects of low SES reduce exposure to the microbial inputs on which we are in a state of evolved dependence, whereas the lifestyle of wealthy citizens maintains these exposures. This partially explains the health deficit of low SES, so focussing on our evolutionary history and on environmental and lifestyle factors that distort microbial exposures might help to mitigate that deficit. But the human microbiota is complex and we have poor understanding of its functions at the microbial and mechanistic levels, and in the brain. Perhaps its composition is more flexible than the microbiota of animals that have restricted habitats and less diverse diets? These uncertainties are discussed in relation to the encouraging but frustrating results of attempts to treat psychiatric disorders by modulating the microbiota.
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Affiliation(s)
- Graham A W Rook
- Centre for Clinical Microbiology, Department of infection, UCL (University College London), London, UK.
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2
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Mazel F, Guisan A, Parfrey LW. Transmission mode and dispersal traits correlate with host specificity in mammalian gut microbes. Mol Ecol 2024; 33:e16862. [PMID: 36786039 DOI: 10.1111/mec.16862] [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: 08/30/2022] [Revised: 11/24/2022] [Accepted: 01/09/2023] [Indexed: 02/15/2023]
Abstract
Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts that specificity levels measured across microbes is correlated to transmission mode (vertical vs. horizontal) and individual dispersal traits. Here, we leverage two large publicly available gut microbiota data sets (1490 samples from 195 host species) to test this prediction. We found that host specificity varies widely across bacteria (i.e., there are generalist and specialist bacteria) and depends on transmission mode and dispersal ability. Horizontally-like transmitted bacteria equipped with traits that facilitate switches between host (e.g., tolerance to oxygen) were found to be less specific (more generalist) than microbes without those traits, for example, vertically-like inherited bacteria that are intolerant to oxygen. Altogether, our findings are compatible with a model in which limited microbial dispersal abilities foster host specificity.
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Affiliation(s)
- Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Field CJ, Bowerman KL, Hugenholtz P. Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli. Microb Genom 2024; 10:001176. [PMID: 38189216 PMCID: PMC10868615 DOI: 10.1099/mgen.0.001176] [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: 10/24/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Many peptidoglycan-deficient bacteria such as the Mycoplasmatales are known host-associated lineages, lacking the environmental resistance mechanisms and metabolic capabilities necessary for a free-living lifestyle. Several peptidoglycan-deficient and non-sporulating orders of interest are thought to be descended from Gram-positive sporulating Bacilli through reductive evolution. Here we annotate 2650 genomes belonging to the class Bacilli, according to the Genome Taxonomy Database, to predict the peptidoglycan and sporulation phenotypes of three novel orders, RFN20, RF39 and ML615J-28, known only through environmental sequence surveys. These lineages are interspersed between peptidoglycan-deficient non-sporulating orders including the Mycoplasmatales and Acholeplasmatales, and more typical Gram-positive orders such as the Erysipelotrichales and Staphylococcales. We use the extant genotypes to perform ancestral state reconstructions. The novel orders are predicted to have small genomes with minimal metabolic capabilities and to comprise a mix of peptidoglycan-deficient and/or non-sporulating species. In contrast to expectations based on cultured representatives, the order Erysipelotrichales lacks many of the genes involved in peptidoglycan and endospore formation. The reconstructed evolutionary history of these traits suggests multiple independent whole-genome reductions and loss of phenotype via intermediate transition states that continue into the present. We suggest that the evolutionary history of the reduced-genome lineages within the class Bacilli is one driven by multiple independent transitions to host-associated lifestyles, with the degree of reduction in environmental resistance and metabolic capabilities correlated with degree of host association.
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Affiliation(s)
- Christian J. Field
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kate L. Bowerman
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
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Ingribelli E, Modrackova N, Tejnecky V, Killer J, Schwab C, Neuzil-Bunesova V. Culture-dependent screening of endospore-forming clostridia in infant feces. BMC Microbiol 2023; 23:347. [PMID: 37978420 PMCID: PMC10655253 DOI: 10.1186/s12866-023-03104-4] [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: 03/09/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Only a few studies dealt with the occurrence of endospore-forming clostridia in the microbiota of infants without obvious health complications. METHODS A methodology pipeline was developed to determine the occurrence of endospore formers in infant feces. Twenty-four fecal samples (FS) were collected from one infant in monthly intervals and were subjected to variable chemical and heat treatment in combination with culture-dependent analysis. Isolates were identified by MALDI-TOF mass spectrometry, 16S rRNA gene sequencing, and characterized with biochemical assays. RESULTS More than 800 isolates were obtained, and a total of 21 Eubacteriales taxa belonging to the Clostridiaceae, Lachnospiraceae, Oscillospiraceae, and Peptostreptococcaceae families were detected. Clostridium perfringens, C. paraputrificum, C. tertium, C. symbiosum, C. butyricum, and C. ramosum were the most frequently identified species compared to the rarely detected Enterocloster bolteae, C. baratii, and C. jeddahense. Furthermore, the methodology enabled the subsequent cultivation of less frequently detectable gut taxa such as Flavonifractor plautii, Intestinibacter bartlettii, Eisenbergiella tayi, and Eubacterium tenue. The isolates showed phenotypic variability regarding enzymatic activity, fermentation profiles, and butyrate production. CONCLUSIONS Taken together, this approach suggests and challenges a cultivation-based pipeline that allows the investigation of the population of endospore formers in complex ecosystems such as the human gastrointestinal tract.
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Affiliation(s)
- Eugenio Ingribelli
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Prague, Czechia
| | - Nikol Modrackova
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Prague, Czechia
| | - Vaclav Tejnecky
- Department of Soil Science and Soil Protection, Czech University of Life Sciences Prague, Prague, Czechia
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Prague, Czechia
- Institute of Animal Physiology and Genetics v.v.i, the Czech Academy of Sciences, Prague, Czechia
| | - Clarissa Schwab
- Biological and Chemical Engineering, Aarhus University, Aarhus C, Denmark
| | - Vera Neuzil-Bunesova
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Prague, Czechia.
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Pavia G, Marascio N, Matera G, Quirino A. Does the Human Gut Virome Contribute to Host Health or Disease? Viruses 2023; 15:2271. [PMID: 38005947 PMCID: PMC10674713 DOI: 10.3390/v15112271] [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: 09/20/2023] [Revised: 11/04/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The human gastrointestinal (GI) tract harbors eukaryotic and prokaryotic viruses and their genomes, metabolites, and proteins, collectively known as the "gut virome". This complex community of viruses colonizing the enteric mucosa is pivotal in regulating host immunity. The mechanisms involved in cross communication between mucosal immunity and the gut virome, as well as their relationship in health and disease, remain largely unknown. Herein, we review the literature on the human gut virome's composition and evolution and the interplay between the gut virome and enteric mucosal immunity and their molecular mechanisms. Our review suggests that future research efforts should focus on unraveling the mechanisms of gut viruses in human homeostasis and pathophysiology and on developing virus-prompted precision therapies.
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Affiliation(s)
| | - Nadia Marascio
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Græcia” University Hospital of Catanzaro, 88100 Catanzaro, Italy
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Treitli SC, Hanousková P, Beneš V, Brune A, Čepička I, Hampl V. Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti. THE ISME JOURNAL 2023; 17:1884-1894. [PMID: 37634049 PMCID: PMC10579272 DOI: 10.1038/s41396-023-01499-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/28/2023]
Abstract
Pelomyxa is a genus of anaerobic amoebae that live in consortia with multiple prokaryotic endosymbionts. Although the symbionts represent a large fraction of the cellular biomass, their metabolic roles have not been investigated. Using single-cell genomics and transcriptomics, we have characterized the prokaryotic community associated with P. schiedti, which is composed of two bacteria, Candidatus Syntrophus pelomyxae (class Deltaproteobacteria) and Candidatus Vesiculincola pelomyxae (class Clostridia), and a methanogen, Candidatus Methanoregula pelomyxae. Fluorescence in situ hybridization and electron microscopy showed that Ca. Vesiculincola pelomyxae is localized inside vesicles, whereas the other endosymbionts occur freely in the cytosol, with Ca. Methanoregula pelomyxae enriched around the nucleus. Genome and transcriptome-based reconstructions of the metabolism suggests that the cellulolytic activity of P. schiedti produces simple sugars that fuel its own metabolism and the metabolism of a Ca. Vesiculincola pelomyxae, while Ca. Syntrophus pelomyxae energy metabolism relies on degradation of butyrate and isovalerate from the environment. Both species of bacteria and the ameba use hydrogenases to transfer the electrons from reduced equivalents to hydrogen, a process that requires a low hydrogen partial pressure. This is achieved by the third endosymbiont, Ca. Methanoregula pelomyxae, which consumes H2 and formate for methanogenesis. While the bacterial symbionts can be successfully eliminated by vancomycin treatment without affecting the viability of the amoebae, treatment with 2-bromoethanesulfonate, a specific inhibitor of methanogenesis, killed the amoebae, indicating the essentiality of the methanogenesis for this consortium.
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Affiliation(s)
- Sebastian C Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42, Vestec, Czech Republic.
| | - Pavla Hanousková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00, Prague 2, Czech Republic
| | - Vladimír Beneš
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Brune
- RG Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00, Prague 2, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42, Vestec, Czech Republic.
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Malesevic M, Stanisavljevic N, Matijasevic D, Curcic J, Tasic V, Tasic S, Kojic M. Metagenomic Analysis of Bacterial Community and Isolation of Representative Strains from Vranjska Banja Hot Spring, Serbia. MICROBIAL ECOLOGY 2023; 86:2344-2356. [PMID: 37222803 DOI: 10.1007/s00248-023-02242-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023]
Abstract
The hot spring Vranjska Banja is the hottest spring on the Balkan Peninsula with a water temperature of 63-95 °C and a pH value of 7.1, in situ. According to the physicochemical analysis, Vranjska Banja hot spring belongs to the bicarbonated and sulfated hyperthermal waters. The structures of microbial community of this geothermal spring are still largely unexplored. In order to determine and monitor the diversity of microbiota of the Vranjska Banja hot spring, a comprehensive culture-independent metagenomic analysis was conducted in parallel with a culture-dependent approach for the first time. Microbial profiling using amplicon sequencing analysis revealed the presence of phylogenetically novel taxa, ranging from species to phyla. Cultivation-based methods resulted in the isolation of 17 strains belonging to the genera Anoxybacillus, Bacillus, Geobacillus, and Hydrogenophillus. Whole-genome sequencing of five representative strains was then performed. The genomic characterization and OrthoANI analysis revealed that the Vranjska Banja hot spring harbors phylogenetically novel species of the genus Anoxybacillus, proving its uniqueness. Moreover, these isolates contain stress response genes that enable them to survive in the harsh conditions of the hot springs. The results of the in silico analysis show that most of the sequenced strains have the potential to produce thermostable enzymes (proteases, lipases, amylases, phytase, chitinase, and glucanase) and various antimicrobial molecules that can be of great importance for industrial, agricultural, and biotechnological applications. Finally, this study provides a basis for further research and understanding of the metabolic potential of these microorganisms.
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Affiliation(s)
- Milka Malesevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia.
| | - Nemanja Stanisavljevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Danka Matijasevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Jovana Curcic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Vukasin Tasic
- Faculty of Informatics and Computing, Singidunum University, Belgrade, Serbia
| | - Srdjan Tasic
- The Academy of Applied Technical and Preschool Studies, Nis, Serbia
| | - Milan Kojic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
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Sinotte VM, Renelies-Hamilton J, Andreu-Sánchez S, Vasseur-Cognet M, Poulsen M. Selective enrichment of founding reproductive microbiomes allows extensive vertical transmission in a fungus-farming termite. Proc Biol Sci 2023; 290:20231559. [PMID: 37848067 PMCID: PMC10581767 DOI: 10.1098/rspb.2023.1559] [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: 07/11/2023] [Accepted: 09/09/2023] [Indexed: 10/19/2023] Open
Abstract
Mutualistic coevolution can be mediated by vertical transmission of symbionts between host generations. Termites host complex gut bacterial communities with evolutionary histories indicative of mixed-mode transmission. Here, we document that vertical transmission of gut bacterial strains is congruent across parent to offspring colonies in four pedigrees of the fungus-farming termite Macrotermes natalensis. We show that 44% of the offspring colony microbiome, including more than 80 bacterial genera and pedigree-specific strains, are consistently inherited. We go on to demonstrate that this is achieved because colony-founding reproductives are selectively enriched with a set of non-random, environmentally sensitive and termite-specific gut microbes from their colonies of origin. These symbionts transfer to offspring colony workers with high fidelity, after which priority effects appear to influence the composition of the establishing microbiome. Termite reproductives thus secure transmission of complex communities of specific, co-evolved microbes that are critical to their offspring colonies. Extensive yet imperfect inheritance implies that the maturing colony benefits from acquiring environmental microbes to complement combinations of termite, fungus and vertically transmitted microbes; a mode of transmission that is emerging as a prevailing strategy for hosts to assemble complex adaptive microbiomes.
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Affiliation(s)
- Veronica M. Sinotte
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Justinn Renelies-Hamilton
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark
| | - Sergio Andreu-Sánchez
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark
- Department of Paediatrics, University Medical Centre Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Mireille Vasseur-Cognet
- UMR IRD 242, UPEC, CNRS 7618, UPMC 113, INRAe 1392, Paris 7 113, Institute of Ecology and Environmental Sciences of Paris, Bondy, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark
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Rook GAW. The old friends hypothesis: evolution, immunoregulation and essential microbial inputs. FRONTIERS IN ALLERGY 2023; 4:1220481. [PMID: 37772259 PMCID: PMC10524266 DOI: 10.3389/falgy.2023.1220481] [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: 05/10/2023] [Accepted: 08/18/2023] [Indexed: 09/30/2023] Open
Abstract
In wealthy urbanised societies there have been striking increases in chronic inflammatory disorders such as allergies, autoimmunity and inflammatory bowel diseases. There has also been an increase in the prevalence of individuals with systemically raised levels of inflammatory biomarkers correlating with increased risk of metabolic, cardiovascular and psychiatric problems. These changing disease patterns indicate a broad failure of the mechanisms that should stop the immune system from attacking harmless allergens, components of self or gut contents, and that should terminate inappropriate inflammation. The Old Friends Hypothesis postulates that this broad failure of immunoregulation is due to inadequate exposures to the microorganisms that drive development of the immune system, and drive the expansion of components such as regulatory T cells (Treg) that mediate immunoregulatory mechanisms. An evolutionary approach helps us to identify the organisms on which we are in a state of evolved dependence for this function (Old Friends). The bottom line is that most of the organisms that drive the regulatory arm of the immune system come from our mothers and family and from the natural environment (including animals) and many of these organisms are symbiotic components of a healthy microbiota. Lifestyle changes that are interrupting our exposure to these organisms can now be identified, and many are closely associated with low socioeconomic status (SES) in wealthy countries. These insights will facilitate the development of education, diets and urban planning that can correct the immunoregulatory deficit, while simultaneously reducing other contributory factors such as epithelial damage.
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Affiliation(s)
- Graham A. W. Rook
- Centre for Clinical Microbiology, Department of Infection, UCL (University College London), London, United Kingdom
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Wang Y, Zhou J, Ye J, Sun Z, He Y, Zhao Y, Ren S, Zhang G, Liu M, Zheng P, Wang G, Yang J. Multi-omics reveal microbial determinants impacting the treatment outcome of antidepressants in major depressive disorder. MICROBIOME 2023; 11:195. [PMID: 37641148 PMCID: PMC10464022 DOI: 10.1186/s40168-023-01635-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/30/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND There is a growing body of evidence suggesting that disturbance of the gut-brain axis may be one of the potential causes of major depressive disorder (MDD). However, the effects of antidepressants on the gut microbiota, and the role of gut microbiota in influencing antidepressant efficacy are still not fully understood. RESULTS To address this knowledge gap, a multi-omics study was undertaken involving 110 MDD patients treated with escitalopram (ESC) for a period of 12 weeks. This study was conducted within a cohort and compared to a reference group of 166 healthy individuals. It was found that ESC ameliorated abnormal blood metabolism by upregulating MDD-depleted amino acids and downregulating MDD-enriched fatty acids. On the other hand, the use of ESC showed a relatively weak inhibitory effect on the gut microbiota, leading to a reduction in microbial richness and functions. Machine learning-based multi-omics integrative analysis revealed that gut microbiota contributed to the changes in plasma metabolites and was associated with several amino acids such as tryptophan and its gut microbiota-derived metabolite, indole-3-propionic acid (I3PA). Notably, a significant correlation was observed between the baseline microbial richness and clinical remission at week 12. Compared to non-remitters, individuals who achieved remission had a higher baseline microbial richness, a lower dysbiosis score, and a more complex and well-organized community structure and bacterial networks within their microbiota. These findings indicate a more resilient microbiota community in remitters. Furthermore, we also demonstrated that it was not the composition of the gut microbiota itself, but rather the presence of sporulation genes at baseline that could predict the likelihood of clinical remission following ESC treatment. The predictive model based on these genes revealed an area under the curve (AUC) performance metric of 0.71. CONCLUSION This study provides valuable insights into the role of the gut microbiota in the mechanism of ESC treatment efficacy for patients with MDD. The findings represent a significant advancement in understanding the intricate relationship among antidepressants, gut microbiota, and the blood metabolome. Additionally, this study offers a microbiota-centered perspective that can potentially improve antidepressant efficacy in clinical practice. By shedding light on the interplay between these factors, this research contributes to our broader understanding of the complex mechanisms underlying the treatment of MDD and opens new avenues for optimizing therapeutic approaches. Video Abstract.
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Affiliation(s)
- Yaping Wang
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Jingjing Zhou
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Junbin Ye
- Beijing WeGenome Paradigm Co., Ltd, Beijing, China
| | - Zuoli Sun
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Yi He
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Yingxin Zhao
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Siyu Ren
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Guofu Zhang
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Min Liu
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Peng Zheng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
- NHC Key Laboratory of Diagnosis and Treatment On Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Gang Wang
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China.
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China.
| | - Jian Yang
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088, China.
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China.
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Vittoria M, Saggese A, Isticato R, Baccigalupi L, Ricca E. Probiotics as an Alternative to Antibiotics: Genomic and Physiological Characterization of Aerobic Spore Formers from the Human Intestine. Microorganisms 2023; 11:1978. [PMID: 37630538 PMCID: PMC10458579 DOI: 10.3390/microorganisms11081978] [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: 07/07/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023] Open
Abstract
A total of thirty-two aerobic spore former strains were isolated from intestinal samples of healthy children and analyzed for their hemolytic and antibiotic-resistant activities. Four strains selected as non-hemolytic and sensitive to all antibiotics recommended as relevant by regulatory agencies were short-listed and evaluated for their in silico and in vitro probiotic potentials. The four selected strains were assigned to the Bacillus velezensis (MV4 and MV11), B. subtilis (MV24), and Priestia megaterium (formerly Bacillus megaterium) (MV30) species. A genomic analysis indicated that MV4, MV11, and MV24 contained a homolog of the gene coding for the fibrinolytic enzyme nattokinase while only MV30 encoded a glutamic acid decarboxylase essential to synthesize the neurotransmitter GABA. All four strains contained gene clusters potentially coding for new antimicrobials, showed strong antioxidant activity, formed biofilm, and produced/secreted quorum-sensing peptides able to induce a cytoprotective stress response in a model of human intestinal (HT-29) cells. Altogether, genomic and physiological data indicate that the analyzed strains do not pose safety concerns and have in vitro probiotic potentials allowing us to propose their use as an alternative to antibiotics.
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Affiliation(s)
- Maria Vittoria
- Department of Biology, Federico II University of Naples, 80125 Naples, Italy; (M.V.); (A.S.); (R.I.)
| | - Anella Saggese
- Department of Biology, Federico II University of Naples, 80125 Naples, Italy; (M.V.); (A.S.); (R.I.)
| | - Rachele Isticato
- Department of Biology, Federico II University of Naples, 80125 Naples, Italy; (M.V.); (A.S.); (R.I.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy;
| | - Loredana Baccigalupi
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy;
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, 80131 Naples, Italy
| | - Ezio Ricca
- Department of Biology, Federico II University of Naples, 80125 Naples, Italy; (M.V.); (A.S.); (R.I.)
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Montagnani M, Bottalico L, Potenza MA, Charitos IA, Topi S, Colella M, Santacroce L. The Crosstalk between Gut Microbiota and Nervous System: A Bidirectional Interaction between Microorganisms and Metabolome. Int J Mol Sci 2023; 24:10322. [PMID: 37373470 DOI: 10.3390/ijms241210322] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Several studies have shown that the gut microbiota influences behavior and, in turn, changes in the immune system associated with symptoms of depression or anxiety disorder may be mirrored by corresponding changes in the gut microbiota. Although the composition/function of the intestinal microbiota appears to affect the central nervous system (CNS) activities through multiple mechanisms, accurate epidemiological evidence that clearly explains the connection between the CNS pathology and the intestinal dysbiosis is not yet available. The enteric nervous system (ENS) is a separate branch of the autonomic nervous system (ANS) and the largest part of the peripheral nervous system (PNS). It is composed of a vast and complex network of neurons which communicate via several neuromodulators and neurotransmitters, like those found in the CNS. Interestingly, despite its tight connections to both the PNS and ANS, the ENS is also capable of some independent activities. This concept, together with the suggested role played by intestinal microorganisms and the metabolome in the onset and progression of CNS neurological (neurodegenerative, autoimmune) and psychopathological (depression, anxiety disorders, autism) diseases, explains the large number of investigations exploring the functional role and the physiopathological implications of the gut microbiota/brain axis.
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Affiliation(s)
- Monica Montagnani
- Department of Precision and Regenerative Medicine and Ionian Area-Section of Pharmacology, School of Medicine, University of Bari "Aldo Moro", Policlinico University Hospital of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Lucrezia Bottalico
- School of Technical Medical Sciences, "Alexander Xhuvani" University of Elbasan, 3001-3006 Elbasan, Albania
| | - Maria Assunta Potenza
- Department of Precision and Regenerative Medicine and Ionian Area-Section of Pharmacology, School of Medicine, University of Bari "Aldo Moro", Policlinico University Hospital of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Ioannis Alexandros Charitos
- Pneumology and Respiratory Rehabilitation Division, Maugeri Clinical Scientific Research Institutes (IRCCS), 70124 Bari, Italy
| | - Skender Topi
- School of Technical Medical Sciences, "Alexander Xhuvani" University of Elbasan, 3001-3006 Elbasan, Albania
| | - Marica Colella
- Interdisciplinary Department of Medicine, Microbiology and Virology Unit, School of Medicine, University of Bari "Aldo Moro", Piazza G. Cesare, 11, 70124 Bari, Italy
| | - Luigi Santacroce
- Interdisciplinary Department of Medicine, Microbiology and Virology Unit, School of Medicine, University of Bari "Aldo Moro", Piazza G. Cesare, 11, 70124 Bari, Italy
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Xu M, Selvaraj GK, Lu H. Environmental sporobiota: Occurrence, dissemination, and risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161809. [PMID: 36702282 DOI: 10.1016/j.scitotenv.2023.161809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/03/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Spore-forming bacteria known as sporobiota are widespread in diverse environments from terrestrial and aquatic habitats to industrial and healthcare systems. Studies on sporobiota have been mainly focused on food processing and clinical fields, while a large amount of sporobiota exist in natural environments. Due to their persistence and capabilities of transmitting virulence factors and antibiotic resistant genes, environmental sporobiota could pose significant health risks to humans. These risks could increase as global warming and environmental pollution has altered the life cycle of sporobiota. This review summarizes the current knowledge of environmental sporobiota, including their occurrence, characteristics, and functions. An interaction network among clinical-, food-related, and environment-related sporobiota is constructed. Recent and effective methods for detecting and disinfecting environmental sporobiota are also discussed. Key problems and future research needs for better understanding and reducing the risks of environmental sporobiota and sporobiome are proposed.
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Affiliation(s)
- Min Xu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ganesh-Kumar Selvaraj
- Department of Microbiology, St. Peter's Institute of Higher Education and Research, Chennai 600054, Tamil Nadu, India.
| | - Huijie Lu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety, Zhejiang, China.
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14
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Belykh OI, Sorokovikova EG, Tomberg IV, Fedorova GA, Kuzmin AV, Krasnopeev AY, Suslova MY, Potapov SA, Belykh TI, Norovsuren J, Galachyants AD, Tikhonova IV. Water Quality, Toxicity and Diversity of Planktonic and Benthic Cyanobacteria in Pristine Ancient Lake Khubsugul (Hövsgöl), Mongolia. Toxins (Basel) 2023; 15:toxins15030213. [PMID: 36977104 PMCID: PMC10053237 DOI: 10.3390/toxins15030213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
For the first time, microcystin-producing cyanobacteria have been detected in Khubsugul, which is ancient, pristine and one of the world’s largest lakes. The microcystin synthetase genes belonged to the genera Nostoc, Microcystis and possibly Snowella spp. No microcystins were found in the water of the lake. Using the HPLC-HRMS/TOF, five microcystin congeners were identified in biofilms from stony substrates sampled in the coastal zone. The concentration of microcystins in biofilms was low: 41.95 µg g−1 d. wt. by ELISA and 55.8 µg g−1 d. wt. using HPLC. The taxonomic composition of planktonic and benthic cyanobacterial communities was determined by means of microscopy and high-throughput sequencing of 16S rDNA amplicons. Nostocales cyanobacteria dominated benthos of Lake Khubsugul and Synechococcales—plankton. The abundance of cyanobacteria was low both in plankton and benthos; there was no mass development of cyanobacteria. Hydrochemical and microbiological analyses showed that the water in the lake was clean; the number of faecal microorganisms was significantly below the acceptable guideline values. Hydrochemical and hydrophysical parameters, and the concentration of chlorophyll a, were low and within the range of values recorded in the 1970s to 1990s, and corresponded to the oligotrophic state of the lake. There were no signs of anthropogenic eutrophication of the lake and no conditions for the cyanobacterial blooms.
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Affiliation(s)
- Olga I. Belykh
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
- Correspondence: (O.I.B.); (E.G.S.)
| | - Ekaterina G. Sorokovikova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
- Correspondence: (O.I.B.); (E.G.S.)
| | - Irina V. Tomberg
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Galina A. Fedorova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Anton V. Kuzmin
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Andrey Yu. Krasnopeev
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Maria Yu. Suslova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Sergey A. Potapov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Tatiana I. Belykh
- Institute for Culture, Social Communication and Information Technology, Baikal State University, 11 Lenin Str., Irkutsk 664003, Russia
| | - Jadambaa Norovsuren
- Institute of Biology of the Mongolian Academy of Sciences, 54B Peace Avenue, Bayanzurkh District, Ulaanbaatar 13330, Mongolia
| | - Agnia D. Galachyants
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Irina V. Tikhonova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
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15
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Corona Ramírez A, Lee KS, Odriozola A, Kaminek M, Stocker R, Zuber B, Junier P. Multiple roads lead to Rome: unique morphology and chemistry of endospores, exospores, myxospores, cysts and akinetes in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36804869 DOI: 10.1099/mic.0.001299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The production of specialized resting cells is a remarkable survival strategy developed by many organisms to withstand unfavourable environmental factors such as nutrient depletion or other changes in abiotic and/or biotic conditions. Five bacterial taxa are recognized to form specialized resting cells: Firmicutes, forming endospores; Actinobacteria, forming exospores; Cyanobacteria, forming akinetes; the δ-Proteobacterial order Myxococcales, forming myxospores; and Azotobacteraceae, forming cysts. All these specialized resting cells are characterized by low-to-absent metabolic activity and higher resistance to environmental stress (desiccation, heat, starvation, etc.) when compared to vegetative cells. Given their similarity in function, we tested the potential existence of a universal morpho-chemical marker for identifying these specialized resting cells. After the production of endospores, exospores, akinetes and cysts in model organisms, we performed the first cross-species morphological and chemical comparison of bacterial sporulation. Cryo-electron microscopy of vitreous sections (CEMOVIS) was used to describe near-native morphology of the resting cells in comparison to the morphology of their respective vegetative cells. Resting cells shared a thicker cell envelope as their only common morphological feature. The chemical composition of the different specialized resting cells at the single-cell level was investigated using confocal Raman microspectroscopy. Our results show that the different specialized cells do not share a common chemical signature, but rather each group has a unique signature with a variable conservation of the signature of the vegetative cells. Additionally, we present the validation of Raman signatures associated with calcium dipicolinic acid (CaDPA) and their variation across individual cells to develop specific sorting thresholds for the isolation of endospores. This provides a proof of concept of the feasibility of isolating bacterial spores using a Raman-activated cell-sorting platform. This cross-species comparison and the current knowledge of genetic pathways inducing the formation of the resting cells highlights the complexity of this convergent evolutionary strategy promoting bacterial survival.
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Affiliation(s)
- Andrea Corona Ramírez
- Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Kang Soo Lee
- Department of Civil, Institute for Environmental Engineering, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | | | - Marek Kaminek
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Roman Stocker
- Department of Civil, Institute for Environmental Engineering, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Benoît Zuber
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
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16
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Saralegui C, García-Durán C, Romeu E, Hernáez-Sánchez ML, Maruri A, Bastón-Paz N, Lamas A, Vicente S, Pérez-Ruiz E, Delgado I, Luna-Paredes C, Caballero JDD, Zamora J, Monteoliva L, Gil C, del Campo R. Statistical Evaluation of Metaproteomics and 16S rRNA Amplicon Sequencing Techniques for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis. Microbiol Spectr 2022; 10:e0146622. [PMID: 36255300 PMCID: PMC9784762 DOI: 10.1128/spectrum.01466-22] [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: 04/21/2022] [Accepted: 09/23/2022] [Indexed: 01/05/2023] Open
Abstract
Newborn screening for cystic fibrosis (CF) can identify affected but asymptomatic infants. The selection of omic technique for gut microbiota study is crucial due to both the small amount of feces available and the low microorganism load. Our aims were to compare the agreement between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis, including both presence and abundance of taxa, to describe the sequential establishment of the gut microbiota during the first year of life in a small size sample (8 infants and 28 fecal samples). The taxonomic assignations by the two techniques were similar, whereas certain discrepancies were observed in the abundance detection, mostly the lower predicted relative abundance of Bifidobacterium and the higher predicted relative abundance of certain Firmicutes and Proteobacteria by amplicon sequencing. During the first months of life, the CF gut microbiota is characterized by a significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial traits, and the detection of human inflammation-related proteins. Metaproteomics provides information on composition and functionality, as well as data on host-microbiome interactions. Its strength is the identification and quantification of Actinobacteria and certain classes of Firmicutes, but alpha diversity indices are not comparable to those of amplicon sequencing. Both techniques detected an aberrant microbiota in our small cohort of infants with CF during their first year of life, dominated by the enrichment of R. gnavus within a human inflammatory environment. IMPORTANCE In recent years, some techniques have been incorporated for the study of microbial ecosystems, being 16S rRNA gene sequencing being the most widely used. Metaproteomics provides the advantage of identifying the interaction between microorganisms and human cells, but the available databases are less extensive as well as imprecise. Few studies compare the statistical differences between the two techniques to define the composition of an ecosystem. Our work shows that the two methods are comparable in terms of microorganism identification but provide different results in alpha diversity analysis. On the other hand, we have studied newborns with cystic fibrosis, for whom we have described the establishment of an intestinal ecosystem marked by the inflammatory response of the host and the enrichment of Ruminococcus gnavus.
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Affiliation(s)
- Claudia Saralegui
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Carmen García-Durán
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Eduardo Romeu
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Ainhize Maruri
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Natalia Bastón-Paz
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Adelaida Lamas
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Servicio de Pediatría, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Saioa Vicente
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Servicio de Pediatría, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Estela Pérez-Ruiz
- Unidad de Fibrosis Quística, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Isabel Delgado
- Unidad de Fibrosis Quística, Hospital Virgen del Rocío, Seville, Spain
| | - Carmen Luna-Paredes
- Sección de Neumología y Alergia Infantil, Unidad Multidisciplinar Fibrosis Quística, Hospital Doce de Octubre, Madrid, Spain
| | - Juan de Dios Caballero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Javier Zamora
- Unidad de Bioestadística, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria and CIBERESP, Madrid, Spain
| | - Lucía Monteoliva
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | - Concepción Gil
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | - Rosa del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Universidad Alfonso X El Sabio, Madrid, Spain
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17
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Comparative Genomics and Physiological Characterization of Two Aerobic Spore Formers Isolated from Human Ileal Samples. Int J Mol Sci 2022; 23:ijms232314946. [PMID: 36499272 PMCID: PMC9739757 DOI: 10.3390/ijms232314946] [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: 10/19/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Spore formers are ubiquitous microorganisms commonly isolated from most environments, including the gastro-intestinal tract (GIT) of insects and animals. Spores ingested as food and water contaminants safely transit the stomach and reach the intestine, where some of them germinate and temporarily colonize that niche. In the lower part of the GIT, they re-sporulate and leave the body as spores, therefore passing through their entire life cycle in the animal body. In the intestine, both un-germinated spores and germination-derived cells interact with intestinal and immune cells and have health-beneficial effects, which include the production of useful compounds, protection against pathogenic microorganisms, contribution to the development of an efficient immune system and modulation of the gut microbial composition. We report a genomic and physiological characterization of SF106 and SF174, two aerobic spore former strains previously isolated from ileal biopsies of healthy human volunteers. SF106 and SF174 belong respectively to the B. subtilis and Alkalihalobacillus clausii (formerly Bacillus clausii) species, are unable to produce toxins or other metabolites with cytotoxic activity against cultured human cells, efficiently bind mucin and human epithelial cells in vitro and produce molecules with antimicrobial and antibiofilm activities.
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18
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Smrhova T, Jani K, Pajer P, Kapinusova G, Vylita T, Suman J, Strejcek M, Uhlik O. Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis. ENVIRONMENTAL MICROBIOME 2022; 17:48. [PMID: 36089611 PMCID: PMC9465906 DOI: 10.1186/s40793-022-00440-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/26/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND The extreme conditions of thermal springs constitute a unique aquatic habitat characterized by low nutrient contents and the absence of human impacts on the microbial community composition. Thus, these springs may host phylogenetically novel microorganisms with potential use in biotechnology. With this hypothesis in mind, we examined the microbial composition of four thermal springs of the world-renowned spa town of Karlovy Vary (Carlsbad), Czechia, which differ in their temperature and chemical composition. RESULTS Microbial profiling using 16S rRNA gene sequencing revealed the presence of phylogenetically novel taxa at various taxonomic levels, spanning from genera to phyla. Many sequences belonged to novel classes within the phyla Hydrothermae, Altiarchaeota, Verrucomicrobia, and TA06. Cultivation-based methods employing oligotrophic media resulted in the isolation of 44 unique bacterial isolates. These include strains that withstand concentrations of up to 12% NaClw/v in cultivation media or survive a temperature of 100 °C, as well as hitherto uncultured bacterial species belonging to the genera Thermomonas, Paenibacillus, and Cellulomonas. These isolates harbored stress response genes that allow them to thrive in the extreme environment of thermal springs. CONCLUSIONS Our study is the first to analyze the overall microbial community composition of the renowned Karlovy Vary thermal springs. We provide insight into yet another level of uniqueness of these springs. In addition to their unique health benefits and cultural significance, we demonstrate that these springs harbor phylogenetically distinct microorganisms with unusual life strategies. Our findings open up avenues for future research with the promise of a deeper understanding of the metabolic potential of these microorganisms.
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Affiliation(s)
- Tereza Smrhova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Kunal Jani
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, Prague, Czech Republic
| | - Gabriela Kapinusova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Tomas Vylita
- Institute of Balneology and Spa Sciences, Karlovy Vary, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
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19
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Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort. Nat Commun 2022; 13:5252. [PMID: 36068216 PMCID: PMC9448778 DOI: 10.1038/s41467-022-32832-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/17/2022] [Indexed: 11/19/2022] Open
Abstract
Indigenous bacteriophage communities (virome) in the human gut have a huge impact on the structure and function of gut bacterial communities (bacteriome), but virome variation at a population scale is not fully investigated yet. Here, we analyse the gut dsDNA virome in the Japanese 4D cohort of 4198 deeply phenotyped individuals. By assembling metagenomic reads, we discover thousands of high-quality phage genomes including previously uncharacterised phage clades with different bacterial hosts than known major ones. The distribution of host bacteria is a strong determinant for the distribution of phages in the gut, and virome diversity is highly correlated with anti-viral defence mechanisms of the bacteriome, such as CRISPR-Cas and restriction-modification systems. We identify 97 various intrinsic/extrinsic factors that significantly affect the virome structure, including age, sex, lifestyle, and diet, most of which showed consistent associations with both phages and their predicted bacterial hosts. Among the metadata categories, disease and medication have the strongest effects on the virome structure. Overall, these results present a basis to understand the symbiotic communities of bacteria and their viruses in the human gut, which will facilitate the medical and industrial applications of indigenous viruses. Here, Nishijima et al. perform a large-scale analysis of the human gut virome in the Japanese 4D cohort of 4198 deeply phenotyped individuals, revealing thousands of bacteriophage genomes, virus-bacteria interactions, and describing associations with various host and environmental factors.
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20
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Peng M, Wang L, Su H, Zhang L, Yang Y, Sun L, Wu Y, Ran L, Liu S, Yin M, Li S, Chunyu W. Ginsenoside Rg1 improved diabetes through regulating the intestinal microbiota in high‐fat diet and streptozotocin‐induced type 2 diabetes rats. J Food Biochem 2022; 46:e14321. [DOI: 10.1111/jfbc.14321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Man Peng
- Faculty of Basic Medical Science Kunming Medical University Kunming China
| | - Liming Wang
- Faculty of Basic Medical Science Kunming Medical University Kunming China
| | - Hui Su
- Faculty of Basic Medical Science Kunming Medical University Kunming China
- Department of Pharmacy, People's Hospital Affiliated of Shandong First Medical University Jinan China
| | - Lei Zhang
- Faculty of Basic Medical Science Kunming Medical University Kunming China
| | - Yue Yang
- Department of Anesthesiology The Affiliated Hospital of Yunnan University Kunming Yunnan China
| | - Le Sun
- Faculty of Basic Medical Science Kunming Medical University Kunming China
| | - Yi Wu
- Faculty of Basic Medical Science Kunming Medical University Kunming China
| | - Lei Ran
- Faculty of Basic Medical Science Kunming Medical University Kunming China
| | - Sida Liu
- Faculty of Basic Medical Science Kunming Medical University Kunming China
| | - Min Yin
- School of Medicine Yunnan University Kunming China
| | - Shude Li
- Faculty of Basic Medical Science Kunming Medical University Kunming China
| | - Weixun Chunyu
- Faculty of Basic Medical Science Kunming Medical University Kunming China
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21
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Browne HP, Shao Y, Lawley TD. Mother-infant transmission of human microbiota. Curr Opin Microbiol 2022; 69:102173. [PMID: 35785616 DOI: 10.1016/j.mib.2022.102173] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 12/16/2022]
Abstract
Humans are colonised by a highly adapted microbiota with coevolved functions that promote human health, development and disease resistance. Acquisition and assembly of the microbiota start at birth and recent evidence suggests that it coincides with, and informs, immune system development and regulation in the rapidly growing infant. Several large-scale studies have identified Bifidobacterium and Bacteroides species maternally transmitted to infants, many of which are capable of colonising over the longer term. Disruption of maternal transmission by caesarean section and antibiotic exposure around birth is associated with a higher incidence of pathogen colonisation and immune-related disorders in children. In this review, we discuss key maternally transmitted bacterial species, their sources and their potential role in shaping immune development. Maternal transmission of gut bacteria provides a microbial 'starter kit' for infants which promotes healthy growth and disease resistance. Optimising and nurturing this under-appreciated form of kinship should be considered as a priority.
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Affiliation(s)
- Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
| | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
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Lazarević S, Đanic M, Al-Salami H, Mooranian A, Mikov M. Gut Microbiota Metabolism of Azathioprine: A New Hallmark for Personalized Drug-Targeted Therapy of Chronic Inflammatory Bowel Disease. Front Pharmacol 2022; 13:879170. [PMID: 35450035 PMCID: PMC9016117 DOI: 10.3389/fphar.2022.879170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/16/2022] [Indexed: 12/16/2022] Open
Abstract
Despite the growing number of new drugs approved for the treatment of inflammatory bowel disease (IBD), the long-term clinical use of thiopurine therapy and the well-known properties of conventional drugs including azathioprine have made their place in IBD therapy extremely valuable. Despite the fact that thiopurine S-methyltransferase (TPMT) polymorphism has been recognized as a major cause of the interindividual variability in the azathioprine response, recent evidence suggests that there might be some yet unknown causes which complicate dosing strategies causing either failure of therapy or toxicity. Increasing evidence suggests that gut microbiota, with its ability to release microbial enzymes, affects the pharmacokinetics of numerous drugs and subsequently drastically alters clinical effectiveness. Azathioprine, as an orally administered drug which has a complex metabolic pathway, is the prime illustrative candidate for such microbial metabolism of drugs. Comprehensive databases on microbial drug-metabolizing enzymes have not yet been generated. This study provides insights into the current evidence on microbiota-mediated metabolism of azathioprine and systematically accumulates findings of bacteria that possess enzymes required for the azathioprine biotransformation. Additionally, it proposes concepts for the identification of gut bacteria species responsible for the metabolism of azathioprine that could aid in the prediction of dose-response effects, complementing pharmacogenetic approaches already applied in the optimization of thiopurine therapy of IBD. It would be of great importance to elucidate to what extent microbiota-mediated metabolism of azathioprine contributes to the drug outcomes in IBD patients which could facilitate the clinical implementation of novel tools for personalized thiopurine treatment of IBD.
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Affiliation(s)
- Slavica Lazarević
- Department of Pharmacology, Toxicology and Clinical Pharmacology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Maja Đanic
- Department of Pharmacology, Toxicology and Clinical Pharmacology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Hani Al-Salami
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School & Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Armin Mooranian
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School & Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Hearing Therapeutics Department, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia
| | - Momir Mikov
- Department of Pharmacology, Toxicology and Clinical Pharmacology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
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Mechanisms and Applications of Bacterial Sporulation and Germination in the Intestine. Int J Mol Sci 2022; 23:ijms23063405. [PMID: 35328823 PMCID: PMC8953710 DOI: 10.3390/ijms23063405] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Recent studies have suggested a major role for endospore forming bacteria within the gut microbiota, not only as pathogens but also as commensal and beneficial members contributing to gut homeostasis. In this review the sporulation processes, spore properties, and germination processes will be explained within the scope of the human gut. Within the gut, spore-forming bacteria are known to interact with the host’s immune system, both in vegetative cell and spore form. Together with the resistant nature of the spore, these characteristics offer potential for spores’ use as delivery vehicles for therapeutics. In the last part of the review, the therapeutic potential of spores as probiotics, vaccine vehicles, and drug delivery systems will be discussed.
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Abstract
Healthy development and function of essentially all physiological systems and organs, including the brain, require exposure to the microbiota of our mothers and of the natural environment, especially in early life. We also know that some infections, if we survive them, modulate the immune system in relevant ways. If we study the evolution of the immune and metabolic systems, we can understand how these requirements developed and the nature of the organisms that we need to encounter. We can then begin to identify the mechanisms of the beneficial effects of these exposures. Against this evolutionary background, we can analyze the ways in which the modern urban lifestyle, particularly for individuals experiencing low socioeconomic status (SES), results in deficient or distorted microbial exposures and microbiomes. Thus, an evolutionary approach facilitates the identification of practical solutions to the growing scandal of health disparities linked to inequality.
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25
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Linehan K, Dempsey EM, Ryan CA, Ross RP, Stanton C. First encounters of the microbial kind: perinatal factors direct infant gut microbiome establishment. MICROBIOME RESEARCH REPORTS 2022; 1:10. [PMID: 38045649 PMCID: PMC10688792 DOI: 10.20517/mrr.2021.09] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/28/2021] [Accepted: 01/11/2022] [Indexed: 12/05/2023]
Abstract
The human gut microbiome harbors a diverse range of microbes that play a fundamental role in the health and well-being of their host. The early-life microbiome has a major influence on human development and long-term health. Perinatal factors such as maternal nutrition, antibiotic use, gestational age and mode of delivery influence the initial colonization, development, and function of the neonatal gut microbiome. The perturbed early-life gut microbiome predisposes infants to diseases in early and later life. Understanding how perinatal factors guide and shape the composition of the early-life microbiome is essential to improving infant health. The following review provides a synopsis of perinatal factors with the most decisive influences on initial microbial colonization of the infant gut.
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Affiliation(s)
- Kevin Linehan
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Lee Maltings, Cork, Cork T12 YT20, Ireland
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland
| | - Eugene M. Dempsey
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Lee Maltings, Cork, Cork T12 YT20, Ireland
- Department of Paediatrics & Child Health and INFANT Centre, University College Cork, Cork T12 YN60, Ireland
| | - C. Anthony Ryan
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Lee Maltings, Cork, Cork T12 YT20, Ireland
- Department of Paediatrics & Child Health and INFANT Centre, University College Cork, Cork T12 YN60, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Lee Maltings, Cork, Cork T12 YT20, Ireland
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Lee Maltings, Cork, Cork T12 YT20, Ireland
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26
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Chaplin AV, Shcherbakova VA, Pikina AP, Sokolova SR, Korzhanova M, Belova VA, Korostin DO, Rebrikov DV, Kardonsky DA, Urban AS, Zakharzhevskaya NB, Suzina NE, Podoprigora IV, Das MS, Kholopova DO, Efimov BA. Diplocloster agilis gen. nov., sp. nov. and Diplocloster modestus sp. nov., two novel anaerobic fermentative members of Lachnospiraceae isolated from human faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005222] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Three novel strains of Gram-stain-negative, obligately anaerobic, spore-forming straight or slightly curved rods with pointed ends occurring singly or in pairs were isolated from the faeces of healthy human children. The strains were characterized by mesophilic fermentative metabolism and production of acetate, ethanol and H2 as the end metabolic products. Strains ASD3451 and ASD5720T were motile, fermented lactose and raffinose, and weakly fermented maltose. Strain ASD4241T was non-motile and did not ferment the carbohydrates listed above but fermented starch. Strains ASD3451 and ASD5720T shared average nucleotide identity higher than 98.5 % with each other, while ASD4241T had only 88.5-89 % identity to them. Based on phylogenetic and chemotaxonomic analyses, we propose Diplocloster agilis gen. nov., sp. nov. (ASD5720T=JCM 34353T=VKM B-3497T) and Diplocloster modestus sp. nov. (ASD4241T=JCM 34351T=VKM B-3498T) within the family
Lachnospiraceae
.
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Affiliation(s)
- Andrei V. Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Viktoria A. Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research, Russian Academy of Sciences”, Pushchino, Russia
| | - Alla P. Pikina
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofia R. Sokolova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Margarita Korzhanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vera A. Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy O. Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Denis V. Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry A. Kardonsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Anatoly S. Urban
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Natalia B. Zakharzhevskaya
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Natalia E. Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research, Russian Academy of Sciences”, Pushchino, Russia
| | - Irina V. Podoprigora
- Department of Microbiology and Virology, Peoples' Friendship University of Russia, Moscow, Russia
| | - Milana S. Das
- Department of Microbiology and Virology, Peoples' Friendship University of Russia, Moscow, Russia
| | - Daria O. Kholopova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Boris A. Efimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
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27
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López-Moreno A, Ruiz-Moreno Á, Pardo-Cacho J, Cerk K, Torres-Sánchez A, Ortiz P, Úbeda M, Aguilera M. Culturing and Molecular Approaches for Identifying Microbiota Taxa Impacting Children's Obesogenic Phenotypes Related to Xenobiotic Dietary Exposure. Nutrients 2022; 14:nu14020241. [PMID: 35057422 PMCID: PMC8778816 DOI: 10.3390/nu14020241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Integrated data from molecular and improved culturomics studies might offer holistic insights on gut microbiome dysbiosis triggered by xenobiotics, such as obesity and metabolic disorders. Bisphenol A (BPA), a dietary xenobiotic obesogen, was chosen for a directed culturing approach using microbiota specimens from 46 children with obesity and normal-weight profiles. In parallel, a complementary molecular analysis was carried out to estimate the BPA metabolising capacities. Firstly, catalogues of 237 BPA directed-cultured microorganisms were isolated using five selected media and several BPA treatments and conditions. Taxa from Firmicutes, Proteobacteria, and Actinobacteria were the most abundant in normal-weight and overweight/obese children, with species belonging to the genera Enterococcus, Escherichia, Staphylococcus, Bacillus, and Clostridium. Secondly, the representative isolated taxa from normal-weight vs. overweight/obese were grouped as BPA biodegrader, tolerant, or resistant bacteria, according to the presence of genes encoding BPA enzymes in their whole genome sequences. Remarkably, the presence of sporobiota and concretely Bacillus spp. showed the higher BPA biodegradation potential in overweight/obese group compared to normal-weight, which could drive a relevant role in obesity and metabolic dysbiosis triggered by these xenobiotics.
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Affiliation(s)
- Ana López-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
- Microbiota Laboratory, IBS: Instituto de Investigación Biosanitaria ibs, 18012 Granada, Spain
- Correspondence: (A.L.-M.); (M.A.); Tel.: +34-9-5824-5129 (M.A.)
| | - Ángel Ruiz-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Jesús Pardo-Cacho
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
| | - Klara Cerk
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Alfonso Torres-Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Pilar Ortiz
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Marina Úbeda
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
- Microbiota Laboratory, IBS: Instituto de Investigación Biosanitaria ibs, 18012 Granada, Spain
- Correspondence: (A.L.-M.); (M.A.); Tel.: +34-9-5824-5129 (M.A.)
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28
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Exploring the universal healthy human gut microbiota around the World. Comput Struct Biotechnol J 2022; 20:421-433. [PMID: 35035791 PMCID: PMC8749183 DOI: 10.1016/j.csbj.2021.12.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 02/08/2023] Open
Abstract
The human gut holds a special place in the study of different microbial environments due to growing evidence that the gut microbiota is related to host health. However, despite extensive research, there is still a lack of knowledge about the core taxa forming the gut microbiota and, moreover, available information is biased towards western microbiomes in both genome databases and most core taxa studies. To tackle these limitations, we tested a database enrichment strategy and analyzed public datasets of whole-genome shotgun data, generated from 545 fecal samples, comprising three gradients of westernization. The NT database was selected as a baseline of biological diversity, subsequently being combined with various studies of interest related to the human microbiota. This enrichment strategy made it possible to improve classification capacity, compared to the original unenriched database, regarding the various lifestyles and populations studied. The effects of incomplete-taxonomy metagenome-assembled genomes on genome database enrichment were also examined, revealing that, while they are helpful, they should be used with caution depending on the taxonomic level of interest. Moreover, in terms of high prevalence, the core analysis revealed a conserved set of bacterial taxa in the healthy human gut microbiota worldwide, despite apparent lifestyle differences. Such taxa show a set of traits, metabolic roles, and ancestral status, making them suitable candidates for a hypothetical phylogenetic core of mutualistic microorganisms co-evolving with the human species.
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29
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Rosenberg E, Zilber-Rosenberg I. Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations. Microorganisms 2021; 10:microorganisms10010070. [PMID: 35056519 PMCID: PMC8780831 DOI: 10.3390/microorganisms10010070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.
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30
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Abstract
Microorganisms efficiently colonize the external and internal surfaces of the animal body establishing mutually beneficial interactions and forming site- and individual-specific microbiota. The degradation of complex polysaccharides in the animal gut, the production of useful compounds, protection against pathogenic microorganisms and contribution to the development of an efficient immune system are the main beneficial effects of a balanced microbiota. A dysbiosis, an imbalanced composition of the microbiota, has been associated with a large number of diseases from gastro-intestinal or urogenital disorders to allergies, cardiovascular and autoimmune diseases and even to the onset of certain cancers. A growing body of evidence has indicated that probiotic treatments, aimed at maintaining or rebalancing the microbiota, are useful to treat/prevent those illnesses. Lactic Acid Bacteria and Bifidobacteria are the most common microbes used in probiotic preparations; however, other bacteria and yeast cells are also widely used in commercial products. Here we focus on the use of bacterial spore formers as probiotics. Spore formers have been marketed as probiotics for over 50 years and are now extensively used for the treatment of intestinal disorders and as dietary supplements in humans, as growth promoters and competitive exclusion agents in animals.
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31
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Browne HP, Almeida A, Kumar N, Vervier K, Adoum AT, Viciani E, Dawson NJR, Forster SC, Cormie C, Goulding D, Lawley TD. Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle. Genome Biol 2021; 22:204. [PMID: 34348764 PMCID: PMC8340488 DOI: 10.1186/s13059-021-02428-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 07/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Human-to-human transmission of symbiotic, anaerobic bacteria is a fundamental evolutionary adaptation essential for membership of the human gut microbiota. However, despite its importance, the genomic and biological adaptations underpinning symbiont transmission remain poorly understood. The Firmicutes are a dominant phylum within the intestinal microbiota that are capable of producing resistant endospores that maintain viability within the environment and germinate within the intestine to facilitate transmission. However, the impact of host transmission on the evolutionary and adaptive processes within the intestinal microbiota remains unknown. RESULTS We analyze 1358 genomes of Firmicutes bacteria derived from host and environment-associated habitats. Characterization of genomes as spore-forming based on the presence of sporulation-predictive genes reveals multiple losses of sporulation in many distinct lineages. Loss of sporulation in gut Firmicutes is associated with features of host-adaptation such as genome reduction and specialized metabolic capabilities. Consistent with these data, analysis of 9966 gut metagenomes from adults around the world demonstrates that bacteria now incapable of sporulation are more abundant within individuals but less prevalent in the human population compared to spore-forming bacteria. CONCLUSIONS Our results suggest host adaptation in gut Firmicutes is an evolutionary trade-off between transmission range and colonization abundance. We reveal host transmission as an underappreciated process that shapes the evolution, assembly, and functions of gut Firmicutes.
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Affiliation(s)
- Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
| | - Alexandre Almeida
- Wellcome Sanger Institute, Hinxton, UK
- European Bioinformatics Institute, Hinxton, UK
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Kevin Vervier
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | | | - Elisa Viciani
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Nicholas J R Dawson
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | | | | | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
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