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Möller L, Vainshtein Y, Meyer B, Neidhardt J, Eren AM, Sohn K, Rabus R. Rich microbial and depolymerising diversity in Antarctic krill gut. Microbiol Spectr 2024; 12:e0403523. [PMID: 38466097 PMCID: PMC10986584 DOI: 10.1128/spectrum.04035-23] [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: 11/25/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
With almost a quadrillion individuals, the Antarctic krill processes five million tons of organic carbon every day during austral summer. This high carbon flux requires a broad range of hydrolytic enzymes to decompose the diverse food-derived biopolymers. While krill itself possesses numerous such enzymes, it is unclear, to what extent the endogenous microbiota contribute to the hydrolytic potential of the gut environment. Here we applied amplicon sequencing, shotgun metagenomics, cultivation, and physiological assays to characterize the krill gut microbiota. The broad bacterial diversity (273 families, 919 genera, and 2,309 species) also included a complex potentially anaerobic sub-community. Plate-based assays with 198 isolated pure cultures revealed widespread capacities to utilize lipids (e.g., tributyrin), followed by proteins (casein) and to a lesser extent by polysaccharides (e.g., alginate and chitin). While most isolates affiliated with the genera Pseudoalteromonas and Psychrobacter, also Rubritalea spp. (Verrucomicrobia) were observed. The krill gut microbiota growing on marine broth agar plates possess 13,012 predicted hydrolyses; 15-fold more than previously predicted from a transcriptome-proteome compendium of krill. Cultivation-independent and -dependent approaches indicated members of the families Flavobacteriaceae and Pseudoalteromonadaceae to dominate the capacities for lipid/protein hydrolysis and to provide a plethora of carbohydrate-active enzymes, sulfatases, and laminarin- or porphyrin-depolymerizing hydrolases. Notably, also the potential to hydrolyze plastics such as polyethylene terephthalate and polylactatide was observed, affiliating mostly with Moraxellaceae. Overall, this study shows extensive microbial diversity in the krill gut, and suggests that the microbiota likely play a significant role in the nutrient acquisition of the krill by enriching its hydrolytic enzyme repertoire.IMPORTANCEThe Antarctic krill (Euphausia superba) is a keystone species of the Antarctic marine food web, connecting the productivity of phyto- and zooplankton with the nutrition of the higher trophic levels. Accordingly, krill significantly contributes to biomass turnover, requiring the decomposition of seasonally varying plankton-derived biopolymers. This study highlights the likely role of the krill gut microbiota in this ecosystem function by revealing the great number of diverse hydrolases that microbes contribute to the krill gut environment. The here resolved repertoire of hydrolytic enzymes could contribute to the overall nutritional resilience of krill and to the general organic matter cycling under changing environmental conditions in the Antarctic sea water. Furthermore, the krill gut microbiome could serve as a valuable resource of cold-adapted hydrolytic enzymes for diverse biotechnological applications.
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Affiliation(s)
- Lars Möller
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Yevhen Vainshtein
- In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Bettina Meyer
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University Oldenburg (HIFMB), Oldenburg, Germany
- Biosciences, Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - John Neidhardt
- Department of Human Medicine, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - A. Murat Eren
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University Oldenburg (HIFMB), Oldenburg, Germany
- HIFMB-MPG Bridging Group for Marine Genomics, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute (AWI), Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Kai Sohn
- In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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Lin X, Hu T, Wu Z, Li L, Wang Y, Wen D, Liu X, Li W, Liang H, Jin X, Xu X, Wang J, Yang H, Kristiansen K, Xiao L, Zou Y. Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae. IMETA 2024; 3:e174. [PMID: 38882499 PMCID: PMC11170972 DOI: 10.1002/imt2.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/06/2023] [Indexed: 06/18/2024]
Abstract
The Lachnospiraceae family holds promise as a source of next-generation probiotics, yet a comprehensive delineation of its diversity is lacking, hampering the identification of suitable strains for future applications. To address this knowledge gap, we conducted an in-depth genomic and functional analysis of 1868 high-quality genomes, combining data from public databases with our new isolates. This data set represented 387 colonization-selective species-level clusters, of which eight genera represented multilineage clusters. Pan-genome analysis, single-nucleotide polymorphism (SNP) identification, and probiotic functional predictions revealed that species taxonomy, habitats, and geography together shape the functional diversity of Lachnospiraceae. Moreover, analyses of associations with atherosclerotic cardiovascular disease (ACVD) and inflammatory bowel disease (IBD) indicated that several strains of potentially novel Lachnospiraceae species possess the capacity to reduce the abundance of opportunistic pathogens, thereby imparting potential health benefits. Our findings shed light on the untapped potential of novel species enabling knowledge-based selection of strains for the development of next-generation probiotics holding promise for improving human health and disease management.
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Affiliation(s)
- Xiaoqian Lin
- BGI Research Shenzhen China
- School of Bioscience and Biotechnology South China University of Technology Guangzhou China
| | | | - Zhinan Wu
- BGI Research Shenzhen China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | | | | | | | - Xudong Liu
- BGI Research Shenzhen China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Wenxi Li
- BGI Research Shenzhen China
- School of Bioscience and Biotechnology South China University of Technology Guangzhou China
| | | | | | - Xun Xu
- BGI Research Shenzhen China
| | - Jian Wang
- BGI Research Shenzhen China
- James D. Watson Institute of Genome Sciences Hangzhou China
| | - Huanming Yang
- BGI Research Shenzhen China
- James D. Watson Institute of Genome Sciences Hangzhou China
| | - Karsten Kristiansen
- BGI Research Shenzhen China
- Laboratory of Genomics and Molecular Biomedicine University of Copenhagen Copenhagen Denmark
| | - Liang Xiao
- BGI Research Shenzhen China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen Shenzhen China
| | - Yuanqiang Zou
- BGI Research Shenzhen China
- Laboratory of Genomics and Molecular Biomedicine University of Copenhagen Copenhagen Denmark
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen Shenzhen China
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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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Kadowaki R, Tanno H, Maeno S, Endo A. Spore-forming properties and enhanced oxygen tolerance of butyrate-producing Anaerostipes spp. Anaerobe 2023; 82:102752. [PMID: 37301503 DOI: 10.1016/j.anaerobe.2023.102752] [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: 04/20/2023] [Revised: 05/25/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
OBJECTIVES Butyrate producing bacteria are promising candidates for next-generation probiotics. However, they are extremely sensitive to oxygen, which is a significant obstacle to their inclusion in food matrices in a viable form. The present study characterized the spore-forming properties and stress tolerance of human gut butyrate-producing Anaerostipes spp. METHODS Spore formation properties in six species of Anaerostipes spp. were studied by in vitro and in silico tests. RESULTS Spores were observed from the cells of three species using microscopic analyses, while the remaining three did not form spores under the tested conditions. Spore-forming properties were confirmed by an ethanol treatment. The spores of Anaerostipes caccae were tolerant to oxygen and survived for 15 weeks under atmospheric conditions. Spores tolerated heat stress at 70 °C, but not at 80 °C. An in silico analysis of the conservation of potential sporulation signature genes revealed that the majority of human gut butyrate-producing bacteria were classified as potential spore formers. Comparative genomics revealed that three spore-forming Anaerostipes spp. specifically possessed the spore formation-related genes of bkdR, sodA, and splB, which may be key genes for different sporulation properties in Anaerostipes spp. CONCLUSIONS The present study demonstrated the enhanced stress tolerance of butyrate producing Anaerostipes spp. for future probiotic application. Presence of specific gene(s) are possibly keys for sporulation in Anaerostipes spp.
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Affiliation(s)
- Ren Kadowaki
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, 099-2493, Hokkaido, Japan
| | - Hiroki Tanno
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, 099-2493, Hokkaido, Japan
| | - Shintaro Maeno
- Graduate School of Medical Sciences, Kyushu University, 812-8582, Fukuoka, Japan
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, 099-2493, Hokkaido, Japan; Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, 156-8502, Tokyo, Japan.
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Dong Z, Yang J, Tian M, Wang X, Qin X, Huang Q, Wang J. Mechanism of Bile‐Processed Coptidis Rhizoma to Treat Nonalcoholic Fatty Liver Disease in Type 2 Diabetes Mellitus Based on UPLC‐Q‐TOF/MS and Network Pharmacology. ChemistrySelect 2023. [DOI: 10.1002/slct.202204236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Zhaowei Dong
- State Key Laboratory of Southwestern Chinese Medicine Resources Chengdu University of Traditional Chinese Medicine Chengdu China
- College of Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu China
| | - Jingjing Yang
- State Key Laboratory of Southwestern Chinese Medicine Resources Chengdu University of Traditional Chinese Medicine Chengdu China
- College of Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu China
| | - Maoying Tian
- State Key Laboratory of Southwestern Chinese Medicine Resources Chengdu University of Traditional Chinese Medicine Chengdu China
- College of Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu China
| | - Xi Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources Chengdu University of Traditional Chinese Medicine Chengdu China
- College of Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu China
| | - Xiaoyan Qin
- State Key Laboratory of Southwestern Chinese Medicine Resources Chengdu University of Traditional Chinese Medicine Chengdu China
- College of Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu China
| | - Qinwan Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources Chengdu University of Traditional Chinese Medicine Chengdu China
- College of Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu China
| | - Jin Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources Chengdu University of Traditional Chinese Medicine Chengdu China
- College of Ethnic Medicine Chengdu University of Traditional Chinese Medicine Chengdu China
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Vásquez E, Millones C. Isolation and Identification of Bacteria of Genus Bacillus from Composting Urban Solid Waste and Palm Forest in Northern Peru. Microorganisms 2023; 11:microorganisms11030751. [PMID: 36985324 PMCID: PMC10055787 DOI: 10.3390/microorganisms11030751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/26/2023] [Accepted: 03/07/2023] [Indexed: 03/17/2023] Open
Abstract
A technical challenge for composting in Peruvian cities with annual temperatures below 20 °C is that the degradation of municipal solid waste (MSW) is slow, so the identification of cold-adapted bacteria would be interesting for use as inoculants in places with these climatic conditions. This study isolated, identified, and evaluated bacterial strains with cellulolytic and amylolytic activities at low temperatures. Bacterial strains were isolated from the Chachapoyas Municipal Composting Plant and soil from the Ocol Palm Forest in northern Peru. The screening was carried out to evaluate the extracellular enzyme activity of the strains at low temperatures, grouping those with cellulolytic and cellulolytic/amylolytic activities. The DNA-barcoding using 16S rRNA and enzyme activity allowed the identification and selection of five species with enzymatic activity at 15 and 20 °C of the genus Bacillus, three with cellulolytic/amylolytic activity (B. wiedmanii, B. subtilis, and B. velezensis), and two with cellulolytic activity (B. safensis subsp. safensis, and B. subtilis). These strains showed tolerance to temperatures below optimum and could be used in further studies as inoculants for composting organic wastes at temperatures below 20 °C.
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Rasmussen TS, Koefoed AK, Deng L, Muhammed MK, Rousseau GM, Kot W, Sprotte S, Neve H, Franz CMAP, Hansen AK, Vogensen FK, Moineau S, Nielsen DS. CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice. THE ISME JOURNAL 2023; 17:432-442. [PMID: 36631688 PMCID: PMC9938214 DOI: 10.1038/s41396-023-01358-4] [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: 05/20/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023]
Abstract
Many bacteria and archaea harbor the adaptive CRISPR-Cas system, which stores small nucleotide fragments from previous invasions of nucleic acids via viruses or plasmids. This molecular archive blocks further invaders carrying identical or similar nucleotide sequences. However, few of these systems have been confirmed experimentally to be active in gut bacteria. Here, we demonstrate experimentally that the type I-C CRISPR-Cas system of the prevalent gut bacterium Eggerthella lenta can specifically target and cleave foreign DNA in vitro by using a plasmid transformation assay. We also show that the CRISPR-Cas system acquires new immunities (spacers) from the genome of a virulent E. lenta phage using traditional phage assays in vitro but also in vivo using gnotobiotic (GB) mice. Both high phage titer and an increased number of spacer acquisition events were observed when E. lenta was exposed to a low multiplicity of infection in vitro, and three phage genes were found to contain protospacer hotspots. Fewer new spacer acquisitions were detected in vivo than in vitro. Longitudinal analysis of phage-bacteria interactions showed sustained coexistence in the gut of GB mice, with phage abundance being approximately one log higher than the bacteria. Our findings show that while the type I-C CRISPR-Cas system is active in vitro and in vivo, a highly virulent phage in vitro was still able to co-exist with its bacterial host in vivo. Taken altogether, our results suggest that the CRISPR-Cas defense system of E. lenta provides only partial immunity in the gut.
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark.
| | - Anna Kirstine Koefoed
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Ling Deng
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Musemma K Muhammed
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de 1enie, Université Laval, Québec, QC, G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Witold Kot
- Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103, Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103, Kiel, Germany
| | - Axel Kornerup Hansen
- Section of Experimental Animal Models, Department of Veterinary and Animal Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Finn Kvist Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de 1enie, Université Laval, Québec, QC, G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Dennis Sandris Nielsen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark.
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Abstract
Transmission of bacterial endospores between the environment and people and the following germination in vivo play critical roles in both the deadly infections of some bacterial pathogens and the stabilization of the commensal microbiotas in humans. Our knowledge about the germination process of different bacteria in the mammalian gut, however, is still very limited due to the lack of suitable tools to visually monitor this process. We proposed a two-step labeling strategy that can image and quantify the endospores' germination in the recipient's intestines. Endospores collected from donor's gut microbiota were first labeled with fluorescein isothiocyanate and transplanted to mice via gavage. The recipient mice were then administered with Cyanine5-tagged D-amino acid to label all the viable bacteria, including the germinated endospores, in their intestines in situ. The germinated donor endospores could be distinguished by presenting two types of fluorescent signals simultaneously. The integrative use of cell-sorting, 16S rDNA sequencing, and fluorescence in situ hybridization (FISH) staining of the two-colored bacteria unveiled the taxonomic information of the donor endospores that germinated in the recipient's gut. Using this strategy, we investigated effects of different germinants and pre-treatment interventions on their germination, and found that germination of different commensal bacterial genera was distinctly affected by various types of germinants. This two-color labeling strategy shows its potential as a versatile tool for visually monitoring endospore germination in the hosts and screening for new interventions to improve endospore-based therapeutics.
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Affiliation(s)
- Ningning Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liyuan Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yahui Du
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Huibin Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Song
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China,CONTACT Chaoyong Yang
| | - Wei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Wei Wang Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai200127, China
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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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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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Onizuka S, Tanaka M, Mishima R, Nakayama J. Cultivation of Spore-Forming Gut Microbes Using a Combination of Bile Acids and Amino Acids. Microorganisms 2021; 9:1651. [PMID: 34442730 PMCID: PMC8401671 DOI: 10.3390/microorganisms9081651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 12/16/2022] Open
Abstract
Spores of certain species belonging to Firmicutes are efficiently germinated by nutrient germinators, such as amino acids, in addition to bile acid. We attempted to culture difficult-to-culture or yet-to-be cultured spore-forming intestinal bacteria, using a combination of bile acids and amino acids. The combination increased the number of colonies that formed on agar medium plated with ethanol-treated feces. The operational taxonomic units of these colonized bacteria were classified into two types. One type was colonized only by the bile acid (BA) mixture and the other type was colonized using amino acids, in addition to the BA mixture. The latter contained 13 species, in addition to 14 species of the former type, which mostly corresponds to anaerobic difficult-to-culture Clostridiales species, including several new species candidates. The use of a combination of BAs and amino acids effectively increased the culturability of spore-forming intestinal bacteria.
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Affiliation(s)
| | | | | | - Jiro Nakayama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan; (S.O.); (M.T.); (R.M.)
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Kubasova T, Seidlerova Z, Rychlik I. Ecological Adaptations of Gut Microbiota Members and Their Consequences for Use as a New Generation of Probiotics. Int J Mol Sci 2021; 22:5471. [PMID: 34067354 PMCID: PMC8196900 DOI: 10.3390/ijms22115471] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022] Open
Abstract
In this review, we link ecological adaptations of different gut microbiota members with their potential for use as a new generation of probiotics. Gut microbiota members differ in their adaptations to survival in aerobic environments. Interestingly, there is an inverse relationship between aerobic survival and abundance or potential for prolonged colonization of the intestinal tract. Facultative anaerobes, aerotolerant Lactobacilli and endospore-forming Firmicutes exhibit high fluctuation, and if such bacteria are to be used as probiotics, they must be continuously administered to mimic their permanent supply from the environment. On the other hand, species not expressing any form of aerobic resistance, such as those from phylum Bacteroidetes, commonly represent host-adapted microbiota members characterized by vertical transmission from mothers to offspring, capable of long-term colonization following a single dose administration. To achieve maximal probiotic efficacy, the mode of their administration should thus reflect their natural ecology.
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Affiliation(s)
| | | | - Ivan Rychlik
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (T.K.); (Z.S.)
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