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Romero-Rodríguez A, Ruíz-Villafán B, Sánchez S, Paredes-Sabja D. Is there a role for intestinal sporobiota in the antimicrobial resistance crisis? Microbiol Res 2024; 288:127870. [PMID: 39173554 DOI: 10.1016/j.micres.2024.127870] [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: 06/04/2024] [Revised: 07/23/2024] [Accepted: 08/06/2024] [Indexed: 08/24/2024]
Abstract
Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of "silent" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.
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Affiliation(s)
- A Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Ciudad de México 04510, Mexico.
| | - B Ruíz-Villafán
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - S Sánchez
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - D Paredes-Sabja
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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2
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Chen LJ, Li ZZ, Liu W, Lyu B. Impact of high temperature and drought stress on the microbial community in wolf spiders. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116801. [PMID: 39083866 DOI: 10.1016/j.ecoenv.2024.116801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/11/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
High temperatures and drought present significant abiotic challenges that can limit the survival of many arthropods, including wolf spiders, which are ectothermic and play a crucial role in controlling pest populations. However, the impact of these stress factors on the microbiota of spiders remains poorly understood. In this study, we utilized 16 S rRNA gene sequencing to explore the diversity and composition of bacterial communities within Pardosa pseudoannulata under conditions of high temperature and drought stress. We found that Firmicutes, Bacteroidetes, and Proteobacteria were the predominant bacterial phyla present. Analyses of alpha diversity indicated an increase in bacterial diversity under combined stress conditions, as reflected by various diversity indices such as Ace, Chao1, Shannon, and Simpson. Furthermore, co-occurrence network analysis highlighted intricate interactions among the microbial taxa (e.g., Enterobacter, Chitinophaga, and Eubacterium), revealing the adaptive complexity of the spider's microbiome to environmental stress. Functional prediction analysis suggested that combined stress conditions might enhance key metabolic pathways, particularly those related to oxidative phosphorylation and amino acid metabolism. Using Random Forest analysis, we determined that changes in three heat shock proteins were largely attributed to variations in bacterial communities, with Firmicutes being notably influential. Collectively, this in-depth analysis offers novel insights into the responses of microbial communities within spider microbiomes to combined abiotic stresses, providing valuable information for understanding extreme climate impacts and informing ecological management strategies.
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Affiliation(s)
- Li-Jun Chen
- College of Agriculture and Forestry Ecology, Shaoyang University, Shaoyang 422000, China.
| | - Zhe-Zhi Li
- College of Agriculture and Forestry Ecology, Shaoyang University, Shaoyang 422000, China
| | - Wei Liu
- College of Urban and Environment Sciences, Hunan University of Technology, Zhuzhou 412007, China
| | - Bo Lyu
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA.
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3
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Gao J, Fan Y, Lu C, Zhao X, He X. The baicalein amorphous solid dispersion to enhance the dissolution and bioavailability and effects on growth performance, meat quality, antioxidant capacity and intestinal flora in Taihang chickens. Poult Sci 2024; 103:103768. [PMID: 38703758 PMCID: PMC11079524 DOI: 10.1016/j.psj.2024.103768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 05/06/2024] Open
Abstract
Baicalein (BAI) is a natural flavonoid with antioxidant, antitumor and antibacterial properties. However, the bioavailability of BAI was limited due to low solubility. This study aims to improve the solubility of BAI through the amorphous solid dispersion (ASD) and evaluate changes in its pharmacokinetics and pharmacodynamics in Taihang chickens. Polyethylene caprolactam-polyvinyl acetate-polyethylene glycol grafted copolymer (Soluplus) was chosen as the carrier, and ASD was prepared by rotary evaporation and was characterized by powder X-ray diffractions (PXRD), differential scanning calorimetry (DSC) and fourier transform infrared spectroscopy (FT-IR). In vitro dissolution assays were used to screen the optimal ratio of drug to carrier, in vivo pharmacokinetic assays were conducted to investigate the promoting effect on the absorption. In addition, the effects of ASD on the growth performance, meat quality, antioxidant capacity and intestinal flora were investigated. ASD (1:9 and 2:8) did not exhibit crystal diffraction peaks of BAI in PXRD or endothermic peaks in DSC, indicating the successful preparation of ASD. The results of in vitro dissolution assay showed that the cumulative dissolution rate of ASD (2:8) within 600 min was 52.67%, which was 7.84-fold higher than BAI. The pharmacokinetic results showed that the peak concentration (Cmax) and the area under the drug-time curve (AUC0∼24) of ASD (2:8) was (5.20 ± 0.82) μg/mL and (17.03 ± 0.67) μg·h/mL, which was 1.91 and 2.64-fold higher than BAI, respectively. Dietary supplementation of BAI and ASD could increase average daily gain (ADG), while decrease feed conversion ratio (FCR), but there was no significant difference (P > 0.05). The drip loss of BAIASD group was lower than BAI group (P < 0.05). In addition, the antioxidant capacity of Taihang chickens were enhanced, the diversity and the abundance of beneficial bacteria was improved. Results of BAI upon the dietary supplementation tested in Taihang chickens, after preparation of ASD, indicating a superior enhancement effect in growth performance, meat quality, antioxidant capacity and intestinal flora due to an improved solubility and optimized bioavailability.
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Affiliation(s)
- Jianting Gao
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Yingsai Fan
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Chenyue Lu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Xinghua Zhao
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Xin He
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, Hebei 071000, China.
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4
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Carrasco-Acosta M, Garcia-Jimenez P. Development of Multiplex RT qPCR Assays for Simultaneous Detection and Quantification of Faecal Indicator Bacteria in Bathing Recreational Waters. Microorganisms 2024; 12:1223. [PMID: 38930605 PMCID: PMC11205496 DOI: 10.3390/microorganisms12061223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/05/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
In this study, we designed and validated in silico and experimentally a rapid, sensitive, and specific multiplex RT qPCR for the detection and quantification of faecal indicator bacteria (FIB) used as microbiological references in marine bathing water regulations (Escherichia coli and intestinal enterococci). The 16S rRNA gene was used to quantify group-specific enterococci and Escherichia/Shigella and species-specific such as Enterococcus faecalis and E. faecium. Additionally, a ybbW gene encoding allantoin transporter protein was used to detect E. coli. An assessment of marine coastal systems (i.e., marine water and sediment) revealed that intestinal enterococci were the predominant group compared to Escherichia/Shigella. The low contribution of E. faecalis to the intestinal enterococci group was reported. As E. faecalis and E. faecium were reported at low concentrations, it is assumed that other enterococci of faecal origin are contributing to the high gene copy number of this group-specific enterococci. Moreover, low 16S rRNA gene copy numbers with respect to E. faecalis and E. faecium were reported in seawater compared to marine sediment. We conclude that marine sediments can affect the quantification of FIBs included in bathing water regulations. Valuing the quality of the marine coastal system through sediment monitoring is recommended.
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Affiliation(s)
| | - Pilar Garcia-Jimenez
- Department of Biology, Faculty of Marine Sciences, Instituto Universitario de Investigación en Estudios Ambientales y Recursos Naturales i-UNAT, Universidad de Las Palmas de Gran Canaria, 35017 Las Palmas de Gran Canaria, Spain;
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5
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Khairulmunir M, Gani M, Mohd-Ridwan AR, Karuppannan KV, Abdul-Latiff MAB, Md-Zain BM. Alteration of the gut microbial composition of critically endangered Malayan tigers (Panthera tigris jacksoni) in captivity during enrichment phase. Mol Biol Rep 2024; 51:742. [PMID: 38874703 DOI: 10.1007/s11033-024-09642-y] [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: 03/22/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Enrichment activities may influence the microbiomes of captive tigers', affecting their health, digestion, and behavior. Currently, there are few studies that address the impact of enrichment activity on tigers' health. This study aimed to determine the diversity of the gut microbiome in captive Malayan tigers at Zoo Melaka and Night Safari during the environmental enrichment phase using a metabarcoding approach. METHODS AND RESULTS This study utilized different enrichment activities which catered for food, sensory, and cognitive enrichment. Eleven fresh fecal samples from captive Malayan tigers at Zoo Melaka and Night Safari were collected under different conditions. All samples were extracted and 16S rRNA V3-V4 region amplicon sequencing was used to characterize the gut microbiome of captive Malayan tigers subjected to various enrichment activities. Firmicutes, Actinobacteriota, and Fusobacteriota were the dominant phyla observed in the gut microbiome of captive Malayan tigers during enrichment activities. This study revealed β-diversity significantly varied between normal and enrichment phase, however no significant differences were observed in α-diversity. This study demonstrates that environmental enrichment improves the gut microbiome of Malayan tigers because gut microbes such as Lachnoclostridium, which has anti-inflammatory effects and helps maintain homeostasis, and Romboutsia, which has a probiotic effect on the gut microbiome. CONCLUSIONS This study provides valuable insights into the effects of enrichment activities on the gut microbiome of captive Malayan tigers, offering guidance for enhancing captive management practices aimed at promoting the health and well-being of Malayan tiger in captivity.
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Affiliation(s)
- Mohamad Khairulmunir
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN) Peninsular Malaysia, KM 10 Jalan Cheras, Kuala Lumpur, 56100, Malaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, 94300, Malaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN) Peninsular Malaysia, KM 10 Jalan Cheras, Kuala Lumpur, 56100, Malaysia
| | | | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia.
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Goris T, Braune A. Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation. Microb Genom 2024; 10:001245. [PMID: 38785231 PMCID: PMC11170127 DOI: 10.1099/mgen.0.001245] [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: 10/30/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
The genus Catenibacillus (family Lachnospiraceae, phylum Bacillota) includes only one cultivated species so far, Catenibacillus scindens, isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinal Catenibacillus strain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designated Catenibacillus decagia, and showed its ability to deglycosylate C-coupled flavone and xanthone glucosides and O-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome of C. scindens and ten faecal metagenome-assembled genomes assigned to the genus Catenibacillus, we performed a comparative genome analysis and searched for genes encoding potential C-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism of Catenibacillus strains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. Both C. scindens and C. decagia encode a flavonoid O-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoid C-deglycosylation system of Dorea strain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required for C-deglycosylation. The diversity of dgpA and dgpBC gene clusters might explain the broad C-glycoside substrate spectrum of C. scindens and C. decagia. The other Catenibacillus genomes encode only a few potential flavonoid-converting enzymes. Our results indicate that several Catenibacillus species are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.
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Affiliation(s)
- Tobias Goris
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
| | - Annett Braune
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
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7
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Behringer MG, Ho WC, Miller SF, Worthan SB, Cen Z, Stikeleather R, Lynch M. Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine. Curr Biol 2024; 34:1403-1413.e5. [PMID: 38460514 PMCID: PMC11066936 DOI: 10.1016/j.cub.2024.02.040] [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: 10/04/2023] [Revised: 12/12/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
Microbes are evolutionarily robust organisms capable of rapid adaptation to complex stress, which enables them to colonize harsh environments. In nature, microbes are regularly challenged by starvation, which is a particularly complex stress because resource limitation often co-occurs with changes in pH, osmolarity, and toxin accumulation created by metabolic waste. Often overlooked are the additional complications introduced by eventual resource replenishment, as successful microbes must withstand rapid environmental shifts before swiftly capitalizing on replenished resources to avoid invasion by competing species. To understand how microbes navigate trade-offs between growth and survival, ultimately adapting to thrive in environments with extreme fluctuations, we experimentally evolved 16 Escherichia coli populations for 900 days in repeated feast/famine conditions with cycles of 100-day starvation before resource replenishment. Using longitudinal population-genomic analysis, we found that evolution in response to extreme feast/famine is characterized by narrow adaptive trajectories with high mutational parallelism and notable mutational order. Genetic reconstructions reveal that early mutations result in trade-offs for biofilm and motility but trade-ups for growth and survival, as these mutations conferred positively correlated advantages during both short-term and long-term culture. Our results demonstrate how microbes can navigate the adaptive landscapes of regularly fluctuating conditions and ultimately follow mutational trajectories that confer benefits across diverse environments.
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Affiliation(s)
- Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA; Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, 21st Avenue S, Nashville, TN 37232, USA.
| | - Wei-Chin Ho
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA; Department of Biology, University of Texas at Tyler, University Blvd., Tyler, TX 75799, USA.
| | - Samuel F Miller
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
| | - Sarah B Worthan
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA
| | - Zeer Cen
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA
| | - Ryan Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
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8
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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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9
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Karunakaran E, Battarbee R, Tait S, Brentan BM, Berney C, Grinham J, Herrero MA, Omolo R, Douterelo I. Integrating molecular microbial methods to improve faecal pollution management in rivers with designated bathing waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168565. [PMID: 37979848 DOI: 10.1016/j.scitotenv.2023.168565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/23/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
Rivers are at risk from a variety of pollution sources. Faecal pollution is of particular concern since it disperses pathogenic microorganisms in the aquatic environment. Currently, faecal pollution levels in rivers is monitored using faecal indicator bacteria (FIB) that do not offer information about pollution sources and associated risks. This study used a combined molecular approach, along with measurements of water quality, to gain information on pollution sources, and risk levels, in a newly designated recreational bathing site in the River Wharfe (UK). Physico-chemical parameters were monitored in situ, with water quality multiparameter monitoring sondes installed during the 2021 bathing season. The molecular approach was based on quantitative PCR (qPCR)-aided Microbial Source Tracking (MST) and 16S rRNA gene metabarcoding to obtain a fingerprint of bacterial communities and identify potential bioindicators. The analysis from the water quality sondes showed that ammonium was the main parameter determining the distribution of FIB values. Lower faecal pollution levels were detected in the main river when compared to tributaries, except for samples in the river located downstream of a wastewater treatment plant. The faecal pollution type (anthropogenic vs. zoogenic) changed the diversity and the structure of bacterial communities, giving a distinctive fingerprint that can be used to inform source. DNA-based methods showed that the presence of human-derived bacteria was associated with Escherichia coli spikes, coinciding with higher bacterial diversity and the presence of potential pathogenic bacteria mainly of the genus Mycobacterium, Aeromonas and Clostridium. Samples collected after a heavy rainfall event were associated with an increase in Bacteroidales, which are markers of faecal pollution, including Bacteroides graminisolvens, a ruminant marker associated with surface run-off from agricultural sources. The combined use of qPCR and 16S rRNA sequencing was able to identify pollution sources, and novel bacterial indicators, thereby aiding decision-making and management strategies in recreational bathing rivers.
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Affiliation(s)
- Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Rick Battarbee
- Environmental Change Research Centre, University College London, London WC1E 6BT, UK; Addingham Environment Group, Addingham, West Yorkshire LS29 0PD, UK
| | - Simon Tait
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Bruno Melo Brentan
- Hydraulic Engineering and Water Resource Department, Federal University of Minas Gerais, Belo Horizonte 31270, Brazil
| | - Cathal Berney
- Addingham Environment Group, Addingham, West Yorkshire LS29 0PD, UK
| | - James Grinham
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Maria Angeles Herrero
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Ronex Omolo
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Isabel Douterelo
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK.
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10
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Pan Z, Chen Y, Zhou M, McAllister TA, Mcneilly TN, Guan LL. Linking active rectal mucosa-attached microbiota to host immunity reveals its role in host-pathogenic STEC O157 interactions. THE ISME JOURNAL 2024; 18:wrae127. [PMID: 38984791 PMCID: PMC11304501 DOI: 10.1093/ismejo/wrae127] [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: 03/13/2024] [Revised: 05/30/2024] [Accepted: 07/08/2024] [Indexed: 07/11/2024]
Abstract
The rectal-anal junction (RAJ) is the major colonization site of Shiga toxin-producing Escherichia coli (STEC) O157 in beef cattle, leading to transmission of this foodborne pathogen from farms to food chains. To date, there is limited understanding regarding whether the mucosa-attached microbiome has a profound impact on host-STEC interactions. In this study, the active RAJ mucosa-attached microbiota and its potential role in host immunity-STEC commensal interactions were investigated using RAJ mucosal biopsies collected from calves orally challenged with two STEC O157 strains with or without functional stx2a (stx2a+ or stx2a-). The results revealed that shifts of microbial diversity, topology, and assembly patterns were subjected to stx2a production post-challenge and Paeniclostridium and Gallibacterium were the keystone taxa for both microbial interactions and assembly. Additional mucosal transcriptome profiling showed stx2a-dependent host immune responses (i.e. B- and T-cell signaling and antigen processing and presentation) post-challenge. Further integrated analysis revealed that mucosa-attached beneficial microbes (i.e. Provotella, Faecalibacterium, and Dorea) interacted with host immune genes pre-challenge to maintain host homeostasis; however, opportunistic pathogenic microbes (i.e. Paeniclostridium) could interact with host immune genes after the STEC O157 colonization and interactions were stx2a-dependent. Furthermore, predicted bacterial functions involved in pathogen (O157 and Paeniclostridium) colonization and metabolism were related to host immunity. These findings suggest that during pathogen colonization, host-microbe interactions could shift from beneficial to opportunistic pathogenic bacteria driven and be dependent on the production of particular virulence factors, highlighting the potential regulatory role of mucosa-attached microbiota in affecting pathogen-commensal host interactions in calves with STEC O157 infection.
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Affiliation(s)
- Zhe Pan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Yanhong Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB T1J 4B1, Canada
| | - Tom N Mcneilly
- Moredun Research Institute, Penicuik EH26 0PZ, United Kingdom
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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11
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Serrano M, Martins D, Henriques AO. Clostridioides difficile Sporulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:273-314. [PMID: 38175480 DOI: 10.1007/978-3-031-42108-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Some members of the Firmicutes phylum, including many members of the human gut microbiota, are able to differentiate a dormant and highly resistant cell type, the endospore (hereinafter spore for simplicity). Spore-formers can colonize virtually any habitat and, because of their resistance to a wide variety of physical and chemical insults, spores can remain viable in the environment for long periods of time. In the anaerobic enteric pathogen Clostridioides difficile the aetiologic agent is the oxygen-resistant spore, while the toxins produced by actively growing cells are the main cause of the disease symptoms. Here, we review the regulatory circuits that govern entry into sporulation. We also cover the role of spores in the infectious cycle of C. difficile in relation to spore structure and function and the main control points along spore morphogenesis.
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Affiliation(s)
- Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal.
| | - Diogo Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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12
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Fishbein SRS, Mahmud B, Dantas G. Antibiotic perturbations to the gut microbiome. Nat Rev Microbiol 2023; 21:772-788. [PMID: 37491458 DOI: 10.1038/s41579-023-00933-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.
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Affiliation(s)
- Skye R S Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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13
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Marathe A, Zarazúa-Osorio B, Srivastava P, Fujita M. The master regulator for entry into sporulation in Bacillus subtilis becomes a mother cell-specific transcription factor for forespore engulfment. Mol Microbiol 2023; 120:439-461. [PMID: 37485800 DOI: 10.1111/mmi.15132] [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: 12/29/2022] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The Spo0A transcription factor is activated by phosphorylation in starving Bacillus subtilis cells. The activated Spo0A (Spo0A~P) regulates genes controlling entry into sporulation and appears to control mother-cell-specific gene expression after asymmetric division, but the latter remains elusive. Here, we found that Spo0A~P directly binds to three conserved DNA sequences (0A1-3) in the promoter region of the mother cell-specific lytic transglycosylase gene spoIID, which is transcribed by σE -RNA polymerase (RNAP) and negatively controlled by the SpoIIID transcription factor and required for forespore engulfment. Systematic mutagenesis of the 0A boxes revealed that the 0A1 and 0A2 boxes located upstream of the promoter positively control the transcription of spoIID. In contrast, the 0A3 box located downstream of the promoter negatively controls the transcription of spoIID. The mutated SpoIIID binding site located between the -35 and -10 promoter elements causes increased expression of spoIID and reduced sporulation. When the mutations of 0A1, 0A2, and IIID sites are combined, sporulation is restored. Collectively, our data suggest that the mother cell-specific spoIID expression is precisely controlled by the coordination of three factors, Spo0A~P, SpoIIID, and σE -RNAP, for proper sporulation. The conservation of this mechanism across spore-forming species was discussed.
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Affiliation(s)
- Anuradha Marathe
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Priyanka Srivastava
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
- Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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14
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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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15
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Liu Y, Chen S, Wang J, Shao B, Fang J, Cao J. The Phylogeny, Metabolic Potentials, and Environmental Adaptation of an Anaerobe, Abyssisolibacter sp. M8S5, Isolated from Cold Seep Sediments of the South China Sea. Microorganisms 2023; 11:2156. [PMID: 37764000 PMCID: PMC10536192 DOI: 10.3390/microorganisms11092156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Bacillota are widely distributed in various environments, owing to their versatile metabolic capabilities and remarkable adaptation strategies. Recent studies reported that Bacillota species were highly enriched in cold seep sediments, but their metabolic capabilities, ecological functions, and adaption mechanisms in the cold seep habitats remained obscure. In this study, we conducted a systematic analysis of the complete genome of a novel Bacillota bacterium strain M8S5, which we isolated from cold seep sediments of the South China Sea at a depth of 1151 m. Phylogenetically, strain M8S5 was affiliated with the genus Abyssisolibacter within the phylum Bacillota. Metabolically, M8S5 is predicted to utilize various carbon and nitrogen sources, including chitin, cellulose, peptide/oligopeptide, amino acids, ethanolamine, and spermidine/putrescine. The pathways of histidine and proline biosynthesis were largely incomplete in strain M8S5, implying that its survival strictly depends on histidine- and proline-related organic matter enriched in the cold seep ecosystems. On the other hand, strain M8S5 contained the genes encoding a variety of extracellular peptidases, e.g., the S8, S11, and C25 families, suggesting its capabilities for extracellular protein degradation. Moreover, we identified a series of anaerobic respiratory genes, such as glycine reductase genes, in strain M8S5, which may allow it to survive in the anaerobic sediments of cold seep environments. Many genes associated with osmoprotectants (e.g., glycine betaine, proline, and trehalose), transporters, molecular chaperones, and reactive oxygen species-scavenging proteins as well as spore formation may contribute to its high-pressure and low-temperature adaptations. These findings regarding the versatile metabolic potentials and multiple adaptation strategies of strain M8S5 will expand our understanding of the Bacillota species in cold seep sediments and their potential roles in the biogeochemical cycling of deep marine ecosystems.
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Affiliation(s)
- Ying Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535000, China
| | - Songze Chen
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen 518049, China;
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| | - Baoying Shao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
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16
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Arora J, Buček A, Hellemans S, Beránková T, Arias JR, Fisher BL, Clitheroe C, Brune A, Kinjo Y, Šobotník J, Bourguignon T. Evidence of cospeciation between termites and their gut bacteria on a geological time scale. Proc Biol Sci 2023; 290:20230619. [PMID: 37339742 DOI: 10.1098/rspb.2023.0619] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one Cryptocercus cockroach, we show that bacteria endemic to termite guts are mostly transferred vertically. We identified 18 lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for 16 bacterial lineages were within the range of those estimated for 15 mitochondrial genes, suggesting that horizontal transfers are uncommon and vertical transfers are the dominant transmission route in these lineages. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.
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Affiliation(s)
- Jigyasa Arora
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Aleš Buček
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Simon Hellemans
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Tereza Beránková
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Johanna Romero Arias
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Brian L Fisher
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo 101, Madagascar
- California Academy of Sciences, San Francisco, CA, USA
| | - Crystal Clitheroe
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Yukihiro Kinjo
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
- College of Economics and Environmental Policy, Okinawa International University, 2-6-1 Ginowan, Ginowan, 901-2701, Okinawa, Japan
| | - Jan Šobotník
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
- College of Economics and Environmental Policy, Okinawa International University, 2-6-1 Ginowan, Ginowan, 901-2701, Okinawa, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
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17
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Smita N, Anusha R, Indu B, Sasikala C, Ramana CV. In silico analysis of sporulene biosynthesis pathway genes in the members of the class Bacilli. Arch Microbiol 2023; 205:233. [PMID: 37171632 DOI: 10.1007/s00203-023-03558-0] [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: 06/08/2022] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 05/13/2023]
Abstract
Sporulene, a pentacyclic triterpenoid, was discovered in Bacillus subtilis and is associated with bacterial endospores. However, the study was not further extended, leaving a trail of questions. One such question is what diversity of sporulenes exists among spore-forming members? Considering the sporulene biosynthesis pathway as a fundamental tool to survey the distribution of this molecule, a genome mining study was conducted. Mining for genes encoding putative proteins of sporulene biosynthesis pathway among the class Bacilli members revealed the presence of hepS, hepT, ytpB, and sqhC genes in the members of the family Bacillaceae, Caryophanaceae, Paenibacillaceae, and Sporolactobacillaceae. However, these genes were completely absent in the members of Staphylococcaceae, Lactobacillaceae, Aerococcaceae, Carnobacteriaceae, and Leuconostocaceae. Unlike other probable pathway related proteins, a conserved amino acid domain of putative terpenoid cyclase (YtpB) appeared deep-rooted among the genus Bacillus members. In-depth analysis showed the constant gene arrangement of hepS, hepT, ytpB, and sqhC genes in these members, there by demonstrating the conserved nature of sporulene biosynthesis pathway in the members of the genus Bacillus. Our study suggests confinement of the sporulene biosynthesis pathway to spore-forming members of the class Bacilli, majorly to the genus Bacillus.
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Affiliation(s)
- N Smita
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India
| | - R Anusha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India
| | - B Indu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J.N.T. University Hyderabad, Kukatpally, Hyderabad, 500085, India.
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India.
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18
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Wisnoski NI, Lennon JT. Scaling up and down: movement ecology for microorganisms. Trends Microbiol 2023; 31:242-253. [PMID: 36280521 DOI: 10.1016/j.tim.2022.09.016] [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: 06/13/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Movement is critical for the fitness of organisms, both large and small. It dictates how individuals acquire resources, evade predators, exchange genetic material, and respond to stressful environments. Movement also influences ecological and evolutionary dynamics at higher organizational levels, such as populations and communities. However, the links between individual motility and the processes that generate and maintain microbial diversity are poorly understood. Movement ecology is a framework linking the physiological and behavioral properties of individuals to movement patterns across scales of space, time, and biological organization. By synthesizing insights from cell biology, ecology, and evolution, we expand theory from movement ecology to predict the causes and consequences of microbial movements.
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Affiliation(s)
- Nathan I Wisnoski
- Wyoming Geographic Information Science Center, University of Wyoming, Laramie, WY 82071, USA; Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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19
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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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20
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Tian H, Cui J, Ye C, Zhao J, Yang B, Xu Y, Ji S, Wang L, Lv X, Ma C, Zhou S, Li N, Wang X, Qin H, Chen Q. Depletion of butyrate-producing microbes of the Firmicutes predicts nonresponse to FMT therapy in patients with recurrent Clostridium difficile infection. Gut Microbes 2023; 15:2236362. [PMID: 37469017 PMCID: PMC10361143 DOI: 10.1080/19490976.2023.2236362] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/20/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Approximately 10% of individuals diagnosed with Clostridium difficile infection (CDI) show the resistance to fecal microbiota transplantation (FMT), with the underlying mechanisms remaining elusive. Deciphering the intricate microbiome profile within this particular subset of FMT-refractory patients via clinical FMT investigations assumes paramount importance, as it holds the key to designing targeted therapeutic interventions tailored for CDI, particularly recurrent CDI (rCDI). A cohort of twenty-three patients afflicted with rCDI, exhibiting congruent clinical baselines, was meticulously selected for FMT. Rigorous screening of thousands of healthy individuals identified ten FMT donors who met stringent health standards, while a total of 171 stool samples were collected to serve as healthy controls. To assess the influence of microbiome dynamics on FMT efficacy, fecal samples were collected from four donors over a continuous period of twenty-five weeks. After FMT treatment, seven individuals exhibited an inadequate response to FMT. These non-remission patients displayed a significant reduction in α-diversity indexes. Meanwhile, prior to FMT, the abundance of key butyrate-producing Firmicutes bacteria, including Christensenellaceae_R_7_group, Ruminococcaceae_unclassified, Coprococcus_2, Fusicatenibacter, Oscillospira, and Roseburia, were depleted in non-remission patients. Moreover, Burkholderiales_unclassified, Coprococcus_2, and Oscillospira failed to colonize non-remission patients both pre- and post-treatment. Conversely, patients with a favorable FMT response exhibited a higher relative abundance of Veillonella prior to treatment, whereas its depletion was commonly observed in non-remission individuals. Genera interactions in lower effectiveness FMT donors were more similar to those in non-remission patients, and Burkholderiales_unclassified, Coprococcus_2, and Oscillospira were frequently depleted in these lower effectiveness donors. Older patients were not conducive to the colonization of Veillonella, consistent with their poor prognosis after FMT. FMT non-remission rCDI patients exhibited distinct characteristics that hindered the colonization of beneficial butyrate-producing Firmicutes microbes. These findings hold promise in advancing the precision of FMT therapy for rCDI patients.
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Affiliation(s)
- Hongliang Tian
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Jiaqu Cui
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Chen Ye
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Jiangman Zhao
- Department of Bioinformatics, Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Bo Yang
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Yue Xu
- Department of Bioinformatics, Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Shushen Ji
- Department of Bioinformatics, Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Le Wang
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Xiaoqiong Lv
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Chunlian Ma
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Shailan Zhou
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Ning Li
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Xinjun Wang
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
- Research Institute of Intestinal Diseases, Tongji University School of Medicine, Shanghai, China
| | - Huanlong Qin
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
- Research Institute of Intestinal Diseases, Tongji University School of Medicine, Shanghai, China
| | - Qiyi Chen
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Research Center for Digestive Diseases, Tongji University, Shanghai, China
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People’s Hospital of Tongji University, Shanghai, China
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21
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Suzuki TA, Fitzstevens JL, Schmidt VT, Enav H, Huus KE, Ngwese MM, Grießhammer A, Pfleiderer A, Adegbite BR, Zinsou JF, Esen M, Velavan TP, Adegnika AA, Song LH, Spector TD, Muehlbauer AL, Marchi N, Kang H, Maier L, Blekhman R, Ségurel L, Ko G, Youngblut ND, Kremsner P, Ley RE. Codiversification of gut microbiota with humans. Science 2022; 377:1328-1332. [PMID: 36108023 PMCID: PMC10777373 DOI: 10.1126/science.abm7759] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.
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Affiliation(s)
- Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - J. Liam Fitzstevens
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Victor T. Schmidt
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Kelsey E. Huus
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Mirabeau Mbong Ngwese
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Anne Grießhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Anne Pfleiderer
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Bayode R. Adegbite
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Jeannot F. Zinsou
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Meral Esen
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Thirumalaisamy P. Velavan
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Vietnamese German Center for Medical Research, Hanoi, Vietnam
| | - Ayola A. Adegnika
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research, Tübingen, Germany
- Fondation pour la Recherche Scientifique, Cotonou, Bénin
| | - Le Huu Song
- Vietnamese German Center for Medical Research, Hanoi, Vietnam
- 108 Military Central Hospital, Hanoi, Vietnam
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Amanda L. Muehlbauer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Nina Marchi
- Eco-anthropologie, Muséum National d’Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Hyena Kang
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Laure Ségurel
- Eco-anthropologie, Muséum National d’Histoire Naturelle, CNRS, Université de Paris, Paris, France
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, Villeurbanne, France
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Peter Kremsner
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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22
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Pinacho-Guendulain B, Montiel-Castro AJ, Ramos-Fernández G, Pacheco-López G. Social complexity as a driving force of gut microbiota exchange among conspecific hosts in non-human primates. Front Integr Neurosci 2022; 16:876849. [PMID: 36110388 PMCID: PMC9468716 DOI: 10.3389/fnint.2022.876849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The emergent concept of the social microbiome implies a view of a highly connected biological world, in which microbial interchange across organisms may be influenced by social and ecological connections occurring at different levels of biological organization. We explore this idea reviewing evidence of whether increasing social complexity in primate societies is associated with both higher diversity and greater similarity in the composition of the gut microbiota. By proposing a series of predictions regarding such relationship, we evaluate the existence of a link between gut microbiota and primate social behavior. Overall, we find that enough empirical evidence already supports these predictions. Nonetheless, we conclude that studies with the necessary, sufficient, explicit, and available evidence are still scarce. Therefore, we reflect on the benefit of founding future analyses on the utility of social complexity as a theoretical framework.
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Affiliation(s)
- Braulio Pinacho-Guendulain
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Ciudad de México, Mexico
| | - Augusto Jacobo Montiel-Castro
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- *Correspondence: Augusto Jacobo Montiel-Castro,
| | - Gabriel Ramos-Fernández
- Institute for Research on Applied Mathematics and Systems (IIMAS), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Center for Complexity Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Gustavo Pacheco-López
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- Gustavo Pacheco-López,
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23
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Liu L, Ao D, Cai X, Huang P, Cai N, Lin S, Wu B. Early gut microbiota in very low and extremely low birth weight preterm infants with feeding intolerance: a prospective case-control study. J Microbiol 2022; 60:1021-1031. [PMID: 35984614 PMCID: PMC9390111 DOI: 10.1007/s12275-022-2180-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Ling Liu
- Jinan University, Guangzhou, Guangdong, 510000, China
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Dang Ao
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Xiangsheng Cai
- University of the Chinese Academy of Sciences - Shenzhen Hospital, Shenzhen, Guangdong, 518000, China
| | - Peiyi Huang
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Nali Cai
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Shaozhu Lin
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Benqing Wu
- Jinan University, Guangzhou, Guangdong, 510000, China.
- University of the Chinese Academy of Sciences - Shenzhen Hospital, Shenzhen, Guangdong, 518000, China.
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24
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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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25
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Karasova D, Faldynova M, Matiasovicova J, Sebkova A, Crhanova M, Kubasova T, Seidlerova Z, Prikrylova H, Volf J, Zeman M, Babak V, Juricova H, Rajova J, Vlasatikova L, Rysavka P, Rychlik I. Host Species Adaptation of Obligate Gut Anaerobes Is Dependent on Their Environmental Survival. Microorganisms 2022; 10:microorganisms10061085. [PMID: 35744604 PMCID: PMC9229247 DOI: 10.3390/microorganisms10061085] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 01/27/2023] Open
Abstract
The gut microbiota of warm-blooded vertebrates consists of bacterial species belonging to two main phyla; Firmicutes and Bacteroidetes. However, does it mean that the same bacterial species are found in humans and chickens? Here we show that the ability to survive in an aerobic environment is central for host species adaptation. Known bacterial species commonly found in humans, pigs, chickens and Antarctic gentoo penguins are those capable of extended survival under aerobic conditions, i.e., either spore-forming, aerotolerant or facultatively anaerobic bacteria. Such bacteria are ubiquitously distributed in the environment, which acts as the source of infection with similar probability in humans, pigs, chickens, penguins and likely any other warm-blooded omnivorous hosts. On the other hand, gut anaerobes with no specific adaptation for survival in an aerobic environment exhibit host adaptation. This is associated with their vertical transmission from mothers to offspring and long-term colonisation after administration of a single dose. This knowledge influences the design of next-generation probiotics. The origin of aerotolerant or spore-forming probiotic strains may not be that important. On the other hand, if Bacteroidetes and other host-adapted species are used as future probiotics, host preference should be considered.
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Affiliation(s)
- Daniela Karasova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Marcela Faldynova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Jitka Matiasovicova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Alena Sebkova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Magdalena Crhanova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Tereza Kubasova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Zuzana Seidlerova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Hana Prikrylova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Jiri Volf
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Michal Zeman
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Vladimir Babak
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Helena Juricova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Jana Rajova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Lenka Vlasatikova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Petr Rysavka
- Medi Pharma Vision Ltd., 612 00 Brno, Czech Republic;
| | - Ivan Rychlik
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
- Correspondence: ; Tel.: +420-533-331-201
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26
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Ozkan J, Willcox M, Coroneo M. A comparative analysis of the cephalic microbiome: The ocular, aural, nasal/nasopharyngeal, oral and facial dermal niches. Exp Eye Res 2022; 220:109130. [DOI: 10.1016/j.exer.2022.109130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/08/2022] [Accepted: 05/22/2022] [Indexed: 12/12/2022]
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27
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Podlesny D, Arze C, Dörner E, Verma S, Dutta S, Walter J, Fricke WF. Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation. MICROBIOME 2022; 10:53. [PMID: 35337386 PMCID: PMC8951724 DOI: 10.1186/s40168-022-01251-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/24/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND The understanding of how microbiomes assemble, function, and evolve requires metagenomic tools that can resolve microbiota compositions at the strain level. However, the identification and tracking of microbial strains in fecal metagenomes is challenging and available tools variably classify subspecies lineages, which affects their applicability to infer microbial persistence and transfer. RESULTS We introduce SameStr, a bioinformatic tool that identifies shared strains in metagenomes by determining single-nucleotide variants (SNV) in species-specific marker genes, which are compared based on a maximum variant profile similarity. We validated SameStr on mock strain populations, available human fecal metagenomes from healthy individuals and newly generated data from recurrent Clostridioides difficile infection (rCDI) patients treated with fecal microbiota transplantation (FMT). SameStr demonstrated enhanced sensitivity to detect shared dominant and subdominant strains in related samples (where strain persistence or transfer would be expected) when compared to other tools, while being robust against false-positive shared strain calls between unrelated samples (where neither strain persistence nor transfer would be expected). We applied SameStr to identify strains that are stably maintained in fecal microbiomes of healthy adults over time (strain persistence) and that successfully engraft in rCDI patients after FMT (strain engraftment). Taxonomy-dependent strain persistence and engraftment frequencies were positively correlated, indicating that a specific core microbiota of intestinal species is adapted to be competitive both in healthy microbiomes and during post-FMT microbiome assembly. We explored other use cases for strain-level microbiota profiling, as a metagenomics quality control measure and to identify individuals based on the persisting core gut microbiota. CONCLUSION SameStr provides for a robust identification of shared strains in metagenomic sequence data with sufficient specificity and sensitivity to examine strain persistence, transfer, and engraftment in human fecal microbiomes. Our findings identify a persisting healthy adult core gut microbiota, which should be further studied to shed light on microbiota contributions to chronic diseases. Video abstract.
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Affiliation(s)
- Daniel Podlesny
- Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
| | - Cesar Arze
- Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany
- Current address: Ring Therapeutics, Cambridge, MA, USA
| | - Elisabeth Dörner
- Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany
| | - Sandeep Verma
- Division of Gastroenterology, Sinai Hospital of Baltimore, Baltimore, MD, USA
| | - Sudhir Dutta
- Division of Gastroenterology, Sinai Hospital of Baltimore, Baltimore, MD, USA
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland
| | - W Florian Fricke
- Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
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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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Luo J, Du W, Chu S, Xu Y, Zhang Q, Zhang L, Cheng X, Huang W, Cao J, Su Y. Effects of persulfate treatment on the fates of antibiotic resistance genes in waste activated sludge fermentation process and the underlying mechanism. BIORESOURCE TECHNOLOGY 2022; 345:126474. [PMID: 34864181 DOI: 10.1016/j.biortech.2021.126474] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
The occurrence of antibiotic resistance genes (ARGs) in waste activated sludge (WAS) fermentation was investigated with persulfate (PS)-based treatment. ARGs affiliated with multidrug (mexP), macrolide (blaOXA-129), tetracycline (tetB), sulfonamide (sul1), and vancomycin (vanRG) types were significantly decreased by PS/Fe treatment. Mechanistic investigations revealed that PS/Fe possessed oxidating potential and exhibited devastating effects on WAS fermentation. First, PS/Fe promoted cell structure damage, which facilitated ARGs release from potential hosts. A co-occurrence network analysis indicated that Fe/PS suppressed the proliferation of potential host bacteria. In addition, the PS/Fe treatment induced the decreased abundance of certain functional genes involved in pathways associated with ARGs dissemination. Finally, variation partitioning analysis demonstrated that the microbial community structure exhibited more vital effects on ARGs fates than physicochemical factors (i.e., pH and ORP) and gene expression (i.e., two-component system). This work provided a deeper understanding of the critical factors used to determine ARGs fates during WAS fermentation.
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Affiliation(s)
- Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Wei Du
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Siqin Chu
- Shanghai Engineering Research Center of Biotransformation on Organic Solid Waste, School of Ecological and Environmental Sciences. East China Normal University, Shanghai 200241, China
| | - Yulu Xu
- Shanghai Engineering Research Center of Biotransformation on Organic Solid Waste, School of Ecological and Environmental Sciences. East China Normal University, Shanghai 200241, China
| | - Qin Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Le Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Xiaoshi Cheng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Wenxuan Huang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation on Organic Solid Waste, School of Ecological and Environmental Sciences. East China Normal University, Shanghai 200241, China.
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