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Wang N, Yu HJ, Han XY, Li C, Ye RZ, Du LF, Liu YT, Zhang MZ, Shi XY, Zhu DY, Shi W, Jia N, Jiang JF, Sun Y, Zhao L, Cui XM, Cao WC. Genomic characterization of an emerging Rickettsia barbariae isolated from tick eggs in northwestern China. Emerg Microbes Infect 2024; 13:2396870. [PMID: 39193640 DOI: 10.1080/22221751.2024.2396870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/15/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024]
Abstract
The continual emergence of tick-borne rickettsioses has garnered widespread global attention. Candidatus Rickettsia barbariae (Candidatus R. barbariae), which emerged in Italy in 2008, has been detected in humans from northwestern China. However, the lack of Candidatus R. barbariae genome and isolated strains limits the understanding of its biological characteristics and genomic features. Here, we isolated the Rickettsia for the first time from eggs of Rhipicephalus turanicus in northwestern China, and assembled its whole genome after next-generation sequencing, so we modified the proposed name to Rickettsia barbariae (R. barbariae) to conform to the International Code of Nomenclature of Prokaryotes. Phylogenetic analysis based on the whole genome revealed that it was most closely related to the pathogenic Rickettsia parkeri and Rickettsia africae. All virulence factors, present in the pathogenic spotted fever group rickettsiae, were identified in the R. barbariae isolate. These findings highlight the pathogenic potential of R. barbariae and the necessity for enhanced surveillance of the emerging Rickettsia in the human population.
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Affiliation(s)
- Ning Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
| | - Hui-Jun Yu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Xiao-Yu Han
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
| | - Cheng Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Run-Ze Ye
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, People's Republic of China
| | - Li-Feng Du
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Ya-Ting Liu
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
| | - Ming-Zhu Zhang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Xiao-Yu Shi
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
| | - Dai-Yun Zhu
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
| | - Wenqiang Shi
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
| | - Wu-Chun Cao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, AMMS, Beijing, People's Republic of China
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Venkatachalam S, Jabir T, Vipindas PV, Krishnan KP. Ecological significance of Candidatus ARS69 and Gemmatimonadota in the Arctic glacier foreland ecosystems. Appl Microbiol Biotechnol 2024; 108:128. [PMID: 38229335 DOI: 10.1007/s00253-023-12991-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/08/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024]
Abstract
The Gemmatimonadota phylum has been widely detected in diverse natural environments, yet their specific ecological roles in many habitats remain poorly investigated. Similarly, the Candidatus ARS69 phylum has been identified only in a few habitats, and literature on their metabolic functions is relatively scarce. In the present study, we investigated the ecological significance of phyla Ca. ARS69 and Gemmatimonadota in the Arctic glacier foreland (GF) ecosystems through genome-resolved metagenomics. We have reconstructed the first high-quality metagenome-assembled genome (MAG) belonging to Ca. ARS69 and 12 other MAGs belonging to phylum Gemmatimonadota from the three different Arctic GF samples. We further elucidated these two groups phylogenetic lineage and their metabolic function through phylogenomic and pangenomic analysis. The analysis showed that all the reconstructed MAGs potentially belonged to novel species. The MAGs belonged to Ca. ARS69 consist about 8296 gene clusters, of which only about 8% of single-copy core genes (n = 980) were shared among them. The study also revealed the potential ecological role of Ca. ARS69 is associated with carbon fixation, denitrification, sulfite oxidation, and reduction biochemical processes in the GF ecosystems. Similarly, the study demonstrates the widespread distribution of different classes of Gemmatimonadota across wide ranges of ecosystems and their metabolic functions, including in the polar region. KEY POINTS: • Glacier foreland ecosystems act as a natural laboratory to study microbial community structure. • We have reconstructed 13 metagenome-assembled genomes from the soil samples. • All the reconstructed MAGs belonged to novel species with different metabolic processes. • Ca. ARS69 and Gemmatimonadota MAGs were found to participate in carbon fixation and denitrification processes.
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Affiliation(s)
- Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India.
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
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Zhang Y, Chen W, Yuan Y, Liao X, Mi J. Decreasing light exposure increases the abundance of antibiotic resistance genes in the cecum and feces of laying hens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175275. [PMID: 39111271 DOI: 10.1016/j.scitotenv.2024.175275] [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: 06/12/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
The gut microbiome plays a crucial role in maintaining animal health and is influenced by various factors, including light exposure; however, the response in laying hens of the gut microbiome to intermittent light regimes and the related impact on antibiotic resistance genes (ARGs) remain poorly understood. In this study, we divided 20-week-old laying hens into two groups. These groups were exposed to either continuous normal light or intermittent light for 8 weeks. The feces and cecal contents of laying hens were collected for analysis. Metagenomic analysis of both feces and cecal content samples revealed significant shifts in the microbial composition and abundance of ARGs under intermittent light exposure compared to normal light exposure (P < 0.05). Furthermore, metabolomic analysis of the cecal contents revealed substantial alterations in the abundance and composition of ARGs and mobile genetic elements (MGEs) in response to intermittent light exposure (P < 0.05). Network analysis revealed intricate co-occurrence patterns among bacterial communities, metabolites, and ARGs, highlighting correlations between Bacteroidetes species, ARGs, and metabolites. Although certain bacterial species showed differential associations, the dominant bacteria carrying ARGs or MGEs had relatively low numbers, suggesting that other bacterial communities may have had a greater influence on ARG dissemination. Moreover, our observations highlight the crucial role of metabolites as mediators between bacterial communities and ARGs, providing novel insights into the dynamics of antibiotic resistance development. Our findings underscore the impact of intermittent light exposure on ARG proliferation in poultry farming and emphasize interconnections among ARGs, bacterial communities, and metabolic pathways. The results underscore the importance of considering both microbial communities and metabolic processes to understand antibiotic resistance in agricultural settings.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou 730000, China; Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Wenbo Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou 730000, China; Institute of Marine Science, University of Auckland, Auckland, 1010, New Zealand
| | - Yilin Yuan
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xindi Liao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiandui Mi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou 730000, China; Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730000, China.
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Zhang Y, Wang N, Wan J, Jousset A, Jiang G, Wang X, Wei Z, Xu Y, Shen Q. Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting. BIORESOURCE TECHNOLOGY 2024; 410:131309. [PMID: 39159726 DOI: 10.1016/j.biortech.2024.131309] [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: 07/01/2024] [Revised: 08/08/2024] [Accepted: 08/16/2024] [Indexed: 08/21/2024]
Abstract
Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial hosts in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in the resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the One Health initiative.
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Affiliation(s)
- Yaozhong Zhang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Ningqi Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinxing Wan
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Gaofei Jiang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
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Glendinning L, Wu Z, Vervelde L, Watson M, Balic A. Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota. Microb Genom 2024; 10. [PMID: 39222347 DOI: 10.1099/mgen.0.001289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesized that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta diversity of the microbiota, and to the abundance of 40 bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was.
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Affiliation(s)
| | - Zhiguang Wu
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lonneke Vervelde
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal GD Animal Health, Deventer, Netherlands
| | - Mick Watson
- Centre for Digital Innovation, DSM Biotechnology Centre, Delft, Netherlands
- Scotland's Rural College, Peter Wilson Building, King's Buildings, Edinburgh, UK
| | - Adam Balic
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
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Seong HJ, Kim JJ, Kim T, Ahn SJ, Rho M, Lee KJ, Sul WJ. Recovery of 240 metagenome-assembled genomes from coastal mariculture environments in South Korea. Sci Data 2024; 11:902. [PMID: 39164259 PMCID: PMC11336123 DOI: 10.1038/s41597-024-03769-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
The mariculture industry has seen a rapid expansion in recent years due to the increasing global demand for seafood. However, the industry faces challenges from climate change and increased pathogen pressure. Additionally, the chemicals used to enhance mariculture productivity are changing ocean ecosystems. This study analyzed 36 surface-water metagenomes from South Korean mussel, oyster, scallop, and shrimp farms to expand our understanding of aquaculture microbial genetic resources and the potential impacts of these anthropogenic inputs. We recovered 240 non-redundant species-level metagenome-assembled genomes (MAGs), comprising 224 bacteria, 13 archaea, and three eukaryotes. Most MAGs were assigned to Proteobacteria, Bacteroidota, and Actinobacteriota, with 40.7% remaining unclassified at the species level. Among the three eukaryotic MAGs, one was identified as a novel lineage of green algae, highlighting the uncharacterized genetic diversity in mariculture environments. Additionally, 22 prokaryotic MAGs harbored 26 antibiotic and metal resistance genes, with MAGs carrying beta-lactamases being particularly prevalent in most farms. The obtained microbiome data from mariculture environments can be utilized in future studies to foster healthy, sustainable mariculture practices.
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Affiliation(s)
- Hoon Je Seong
- Korean Medicine Data Division, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Jin Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Taeyune Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Sung Jae Ahn
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Mina Rho
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea
| | - Kwang Jun Lee
- Division of Zoonotic and Vector Borne Disease Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea.
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea.
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Salazar-Jaramillo L, de la Cuesta-Zuluaga J, Chica LA, Cadavid M, Ley RE, Reyes A, Escobar JS. Gut microbiome diversity within Clostridia is negatively associated with human obesity. mSystems 2024; 9:e0062724. [PMID: 39012154 PMCID: PMC11334427 DOI: 10.1128/msystems.00627-24] [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: 05/03/2024] [Accepted: 06/06/2024] [Indexed: 07/17/2024] Open
Abstract
Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production. IMPORTANCE The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.
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Affiliation(s)
- Laura Salazar-Jaramillo
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | | | - Luis A. Chica
- Department of Biological Sciences, Max Planck Tandem Group in Computational Biology, Research Group in Computational Biology and Microbial Ecology (BCEM), Universidad de los Andes, Bogota, Colombia
| | - María Cadavid
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Alejandro Reyes
- Department of Biological Sciences, Max Planck Tandem Group in Computational Biology, Research Group in Computational Biology and Microbial Ecology (BCEM), Universidad de los Andes, Bogota, Colombia
- Department of Pathology and Immunology, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Juan S. Escobar
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
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Anderson BD, Sepulveda DE, Nachnani R, Cortez-Resendiz A, Coates MD, Beckett A, Bisanz JE, Kellogg JJ, Raup-Konsavage WM. High Cannabigerol Hemp Extract Moderates Colitis and Modulates the Microbiome in an Inflammatory Bowel Disease Model. J Pharmacol Exp Ther 2024; 390:331-341. [PMID: 39009468 PMCID: PMC11338277 DOI: 10.1124/jpet.124.002204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/21/2024] [Accepted: 06/21/2024] [Indexed: 07/17/2024] Open
Abstract
Cannabis sativa L. has a long history of medicinal use, particularly for gastrointestinal diseases. Patients with inflammatory bowel disease (IBD) report using cannabis to manage their symptoms, despite little data to support the use of cannabis or cannabis products to treat the disease. In this study, we use the well-described dextran sodium sulfate (DSS) model of colitis in mice to assess the impact of commercially available, noneuphorigenic, high cannabigerol (CBG) hemp extract (20 mg/mL cannabigerol, 20.7 mg/mL cannabidiol, 1 mg/mL cannabichromene) on IBD activity and the colonic microbiome. Mice were given 2% DSS in drinking water for 5 days, followed by 2 days of regular drinking water. Over the 7 days, mice were dosed daily with either high CBG hemp extract or matched vehicle control. Daily treatment with high CBG hemp extract dramatically reduces the severity of disease at the histological and organismal levels as measured by decreased disease activity index, increased colon length, and decreases in percent colon tissue damage. 16S rRNA gene sequencing of the fecal microbiota reveals high CBG hemp extract treatment results in alterations in the microbiota that may be beneficial for colitis. Finally, using metabolomic analysis of fecal pellets, we find that mice treated with high CBG hemp extract have a normalization of several metabolic pathways, including those involved in inflammation. Taken together, these data suggest that high CBG hemp extracts may offer a novel treatment option for patients. SIGNIFICANCE STATEMENT: Using the dextran sodium sulfate model of colitis, the authors show that treatment with high cannabigerol hemp extract reduces the severity of symptoms associated with colitis. Additionally, they show that treatment modulates both the fecal microbiota and metabolome with potential functional significance.
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Affiliation(s)
- Benjamin D Anderson
- Departments of Biochemistry and Molecular Biology (B.D.A., A.B.) and Veterinary and Biomedical Sciences (J.J.K.), and One Health Microbiome Center, Huck Life Sciences Institute (J.E.B.), Pennsylvania State University, University Park, Pennsylvania; and Departments of Pharmacology (D.E.S., R.N., A.C.-R., M.D.C., W.M.R.-K.) and Anesthesiology & Perioperative Medicine (D.E.S.), Center for Cannabis & Natural Product Pharmaceutics (D.E.S., R.N., A.C.-R., M.D.C., J.E.B., J.J.K., W.M.R.-K.), and Divison of Gastroenterology & Hepatology, Department of Medicine (M.D.C., J.J.K.), Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Diana E Sepulveda
- Departments of Biochemistry and Molecular Biology (B.D.A., A.B.) and Veterinary and Biomedical Sciences (J.J.K.), and One Health Microbiome Center, Huck Life Sciences Institute (J.E.B.), Pennsylvania State University, University Park, Pennsylvania; and Departments of Pharmacology (D.E.S., R.N., A.C.-R., M.D.C., W.M.R.-K.) and Anesthesiology & Perioperative Medicine (D.E.S.), Center for Cannabis & Natural Product Pharmaceutics (D.E.S., R.N., A.C.-R., M.D.C., J.E.B., J.J.K., W.M.R.-K.), and Divison of Gastroenterology & Hepatology, Department of Medicine (M.D.C., J.J.K.), Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Rahul Nachnani
- Departments of Biochemistry and Molecular Biology (B.D.A., A.B.) and Veterinary and Biomedical Sciences (J.J.K.), and One Health Microbiome Center, Huck Life Sciences Institute (J.E.B.), Pennsylvania State University, University Park, Pennsylvania; and Departments of Pharmacology (D.E.S., R.N., A.C.-R., M.D.C., W.M.R.-K.) and Anesthesiology & Perioperative Medicine (D.E.S.), Center for Cannabis & Natural Product Pharmaceutics (D.E.S., R.N., A.C.-R., M.D.C., J.E.B., J.J.K., W.M.R.-K.), and Divison of Gastroenterology & Hepatology, Department of Medicine (M.D.C., J.J.K.), Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Alonso Cortez-Resendiz
- Departments of Biochemistry and Molecular Biology (B.D.A., A.B.) and Veterinary and Biomedical Sciences (J.J.K.), and One Health Microbiome Center, Huck Life Sciences Institute (J.E.B.), Pennsylvania State University, University Park, Pennsylvania; and Departments of Pharmacology (D.E.S., R.N., A.C.-R., M.D.C., W.M.R.-K.) and Anesthesiology & Perioperative Medicine (D.E.S.), Center for Cannabis & Natural Product Pharmaceutics (D.E.S., R.N., A.C.-R., M.D.C., J.E.B., J.J.K., W.M.R.-K.), and Divison of Gastroenterology & Hepatology, Department of Medicine (M.D.C., J.J.K.), Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Matthew D Coates
- Departments of Biochemistry and Molecular Biology (B.D.A., A.B.) and Veterinary and Biomedical Sciences (J.J.K.), and One Health Microbiome Center, Huck Life Sciences Institute (J.E.B.), Pennsylvania State University, University Park, Pennsylvania; and Departments of Pharmacology (D.E.S., R.N., A.C.-R., M.D.C., W.M.R.-K.) and Anesthesiology & Perioperative Medicine (D.E.S.), Center for Cannabis & Natural Product Pharmaceutics (D.E.S., R.N., A.C.-R., M.D.C., J.E.B., J.J.K., W.M.R.-K.), and Divison of Gastroenterology & Hepatology, Department of Medicine (M.D.C., J.J.K.), Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Aviauna Beckett
- Departments of Biochemistry and Molecular Biology (B.D.A., A.B.) and Veterinary and Biomedical Sciences (J.J.K.), and One Health Microbiome Center, Huck Life Sciences Institute (J.E.B.), Pennsylvania State University, University Park, Pennsylvania; and Departments of Pharmacology (D.E.S., R.N., A.C.-R., M.D.C., W.M.R.-K.) and Anesthesiology & Perioperative Medicine (D.E.S.), Center for Cannabis & Natural Product Pharmaceutics (D.E.S., R.N., A.C.-R., M.D.C., J.E.B., J.J.K., W.M.R.-K.), and Divison of Gastroenterology & Hepatology, Department of Medicine (M.D.C., J.J.K.), Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Jordan E Bisanz
- Departments of Biochemistry and Molecular Biology (B.D.A., A.B.) and Veterinary and Biomedical Sciences (J.J.K.), and One Health Microbiome Center, Huck Life Sciences Institute (J.E.B.), Pennsylvania State University, University Park, Pennsylvania; and Departments of Pharmacology (D.E.S., R.N., A.C.-R., M.D.C., W.M.R.-K.) and Anesthesiology & Perioperative Medicine (D.E.S.), Center for Cannabis & Natural Product Pharmaceutics (D.E.S., R.N., A.C.-R., M.D.C., J.E.B., J.J.K., W.M.R.-K.), and Divison of Gastroenterology & Hepatology, Department of Medicine (M.D.C., J.J.K.), Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Joshua J Kellogg
- Departments of Biochemistry and Molecular Biology (B.D.A., A.B.) and Veterinary and Biomedical Sciences (J.J.K.), and One Health Microbiome Center, Huck Life Sciences Institute (J.E.B.), Pennsylvania State University, University Park, Pennsylvania; and Departments of Pharmacology (D.E.S., R.N., A.C.-R., M.D.C., W.M.R.-K.) and Anesthesiology & Perioperative Medicine (D.E.S.), Center for Cannabis & Natural Product Pharmaceutics (D.E.S., R.N., A.C.-R., M.D.C., J.E.B., J.J.K., W.M.R.-K.), and Divison of Gastroenterology & Hepatology, Department of Medicine (M.D.C., J.J.K.), Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Wesley M Raup-Konsavage
- Departments of Biochemistry and Molecular Biology (B.D.A., A.B.) and Veterinary and Biomedical Sciences (J.J.K.), and One Health Microbiome Center, Huck Life Sciences Institute (J.E.B.), Pennsylvania State University, University Park, Pennsylvania; and Departments of Pharmacology (D.E.S., R.N., A.C.-R., M.D.C., W.M.R.-K.) and Anesthesiology & Perioperative Medicine (D.E.S.), Center for Cannabis & Natural Product Pharmaceutics (D.E.S., R.N., A.C.-R., M.D.C., J.E.B., J.J.K., W.M.R.-K.), and Divison of Gastroenterology & Hepatology, Department of Medicine (M.D.C., J.J.K.), Pennsylvania State University College of Medicine, Hershey, Pennsylvania
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9
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Carlino N, Blanco-Míguez A, Punčochář M, Mengoni C, Pinto F, Tatti A, Manghi P, Armanini F, Avagliano M, Barcenilla C, Breselge S, Cabrera-Rubio R, Calvete-Torre I, Coakley M, Cobo-Díaz JF, De Filippis F, Dey H, Leech J, Klaassens ES, Knobloch S, O'Neil D, Quijada NM, Sabater C, Skírnisdóttir S, Valentino V, Walsh L, Alvarez-Ordóñez A, Asnicar F, Fackelmann G, Heidrich V, Margolles A, Marteinsson VT, Rota Stabelli O, Wagner M, Ercolini D, Cotter PD, Segata N, Pasolli E. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. Cell 2024:S0092-8674(24)00833-X. [PMID: 39214080 DOI: 10.1016/j.cell.2024.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/17/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]
Abstract
Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.
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Affiliation(s)
- Niccolò Carlino
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Aitor Blanco-Míguez
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Michal Punčochář
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Claudia Mengoni
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Pinto
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Alessia Tatti
- Scuola Universitaria Superiore IUSS Pavia, Pavia, Italy; Centre for Agriculture Food Environment, University of Trento, Trento, Italy; Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, Italy
| | - Paolo Manghi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Armanini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Michele Avagliano
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Coral Barcenilla
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Samuel Breselge
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; Department of Biotechnology, Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Inés Calvete-Torre
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain; Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Hrituraj Dey
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - John Leech
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | | | | | | | - Narciso M Quijada
- Austrian Competence Centre for Feed and Food Quality, Safety, and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria; Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria; Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain; Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | | | - Vincenzo Valentino
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Liam Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland
| | | | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Gloria Fackelmann
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Vitor Heidrich
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain; Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Viggó Thór Marteinsson
- Microbiology Research Group, Matís, Reykjavík, Iceland; University of Iceland, Faculty of Food Science and Nutrition, Reykjavík, Iceland
| | - Omar Rota Stabelli
- Centre for Agriculture Food Environment, University of Trento, Trento, Italy; Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, Italy
| | - Martin Wagner
- Austrian Competence Centre for Feed and Food Quality, Safety, and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria; Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy; Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
| | - Edoardo Pasolli
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
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10
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Oh HN, Sul WJ, Son SY, Han SU, Hur H, Lim SG. Effect of Enterotype-Dependent Stability of the Gut Microbiome on Postgastrectomy Malnutrition in Gastric Cancer Patients. Gastroenterology 2024:S0016-5085(24)05347-2. [PMID: 39151706 DOI: 10.1053/j.gastro.2024.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 07/26/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024]
Affiliation(s)
- Han Na Oh
- Department of Surgery, Ajou University School of Medicine, Suwon, Korea; Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon, Korea; Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | - Sang-Yong Son
- Department of Surgery, Ajou University School of Medicine, Suwon, Korea
| | - Sang-Uk Han
- Department of Surgery, Ajou University School of Medicine, Suwon, Korea
| | - Hoon Hur
- Department of Surgery, Ajou University School of Medicine, Suwon, Korea; Department of Biomedical Science, Graduate School of Ajou University, Suwon, Korea.
| | - Sun Gyo Lim
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea.
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11
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An L, Liu X, Wang J, Xu J, Chen X, Liu X, Hu B, Nie Y, Wu XL. Global diversity and ecological functions of viruses inhabiting oil reservoirs. Nat Commun 2024; 15:6789. [PMID: 39117673 PMCID: PMC11310422 DOI: 10.1038/s41467-024-51101-6] [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: 10/27/2023] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Oil reservoirs, being one of the significant subsurface repositories of energy and carbon, host diverse microbial communities affecting energy production and carbon emissions. Viruses play crucial roles in the ecology of microbiomes, however, their distribution and ecological significance in oil reservoirs remain undetermined. Here, we assemble a catalogue encompassing viral and prokaryotic genomes sourced from oil reservoirs. The catalogue comprises 7229 prokaryotic genomes and 3,886 viral Operational Taxonomic Units (vOTUs) from 182 oil reservoir metagenomes. The results show that viruses are widely distributed in oil reservoirs, and 85% vOTUs in oil reservoir are detected in less than 10% of the samples, highlighting the heterogeneous nature of viral communities within oil reservoirs. Through combined microcosm enrichment experiments and bioinformatics analysis, we validate the ecological roles of viruses in regulating the community structure of sulfate reducing microorganisms, primarily through a virulent lifestyle. Taken together, this study uncovers a rich diversity of viruses and their ecological functions within oil reservoirs, offering a comprehensive understanding of the role of viral communities in the biogeochemical cycles of the deep biosphere.
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Affiliation(s)
- Liyun An
- College of architecture and environment, Sichuan University, Chengdu, 610065, China
| | - Xinwu Liu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Jianwei Wang
- College of Engineering, Peking University, Beijing, 100871, China
| | - Jinbo Xu
- School of Earth and Space Sciences, Peking University, Beijing, 100871, China
| | - Xiaoli Chen
- College of Engineering, Peking University, Beijing, 100871, China
- Institute of Ocean Research, Peking University, Beijing, 100871, China
| | - Xiaonan Liu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Bingxin Hu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, 100871, China.
| | - Xiao-Lei Wu
- College of architecture and environment, Sichuan University, Chengdu, 610065, China.
- College of Engineering, Peking University, Beijing, 100871, China.
- School of Earth and Space Sciences, Peking University, Beijing, 100871, China.
- Institute of Ocean Research, Peking University, Beijing, 100871, China.
- Institute of Ecology, Peking University, Beijing, 100871, China.
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12
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Zytnick AM, Gutenthaler-Tietze SM, Aron AT, Reitz ZL, Phi MT, Good NM, Petras D, Daumann LJ, Martinez-Gomez NC. Identification and characterization of a small-molecule metallophore involved in lanthanide metabolism. Proc Natl Acad Sci U S A 2024; 121:e2322096121. [PMID: 39078674 PMCID: PMC11317620 DOI: 10.1073/pnas.2322096121] [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: 01/09/2024] [Accepted: 06/14/2024] [Indexed: 07/31/2024] Open
Abstract
Many bacteria secrete metallophores, low-molecular-weight organic compounds that bind ions with high selectivity and affinity, in order to access essential metals from the environment. Previous work has elucidated the structures and biosynthetic machinery of metallophores specific for iron, zinc, nickel, molybdenum, and copper. No physiologically relevant lanthanide-binding metallophore has been discovered despite the knowledge that lanthanide metals (Ln) have been revealed to be essential cofactors for certain alcohol dehydrogenases across a diverse range of phyla. Here, we report the biosynthetic machinery, the structure, and the physiological relevance of a lanthanophore, methylolanthanin. The structure of methylolanthanin exhibits a unique 4-hydroxybenzoate moiety which has not previously been described in other metallophores. We find that production of methylolanthanin is required for normal levels of Ln accumulation in the methylotrophic bacterium Methylobacterium extorquens AM1, while overexpression of the molecule greatly increases bioaccumulation and adsorption. Our results provide a clearer understanding of how Ln-utilizing bacteria sense, scavenge, and store Ln; essential processes in the environment where Ln are poorly bioavailable. More broadly, the identification of this lanthanophore opens doors for study of how biosynthetic gene clusters are repurposed for additional functions and the complex relationship between metal homeostasis and fitness.
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Affiliation(s)
- Alexa M. Zytnick
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA94720
| | - Sophie M. Gutenthaler-Tietze
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
- Chair of Bioinorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf40225, Germany
| | - Allegra T. Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO80210
| | - Zachary L. Reitz
- Bioinformatics Group, Wageningen University, Wageningen6708PB, The Netherlands
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93117
| | - Manh Tri Phi
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Nathan M. Good
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA94720
| | - Daniel Petras
- Interfaculty Institute of Microbiology and Medicine, Universität Tübingen, Tübingen72074, Germany
| | - Lena J. Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
- Chair of Bioinorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf40225, Germany
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13
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Wang Y, Shu Y, Sun Y, Zeng Q, Zhang W, Bao Z, Ding W. Acute nitrite exposure causes gut microbiota dysbacteriosis and proliferation of pathogenic Photobacterium in shrimp. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116829. [PMID: 39106572 DOI: 10.1016/j.ecoenv.2024.116829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/24/2024] [Accepted: 07/31/2024] [Indexed: 08/09/2024]
Abstract
Nitrite exposure has become a significant concern in the aquaculture industry, posing a severe threat to aquatic animals such as shrimp. While studies have reported the adverse effects of nitrite on shrimp growth, the part played by the gut microbiota in shrimp mortality resulting from nitrite exposure is poorly understood. Here, the effects of nitrite on shrimp gut bacterial community were investigated using 16S rRNA amplicon sequencing, bacterial isolation, genomic analysis, and infection experiments. Compared to the control_healthy group, changes in the bacterial composition of the nitrite_dead group were associated with reduced abundance of specific beneficial bacteria and increased abundance of certain pathogenic bacteria. Notably, members of the Photobacterium genus were found to be significantly enriched in the nitrite_dead group. Genomic analysis of a representative Photobacterium strain (LvS-8n3) revealed a variety of genes encoding bacterial toxins, including hemolysin, adhesin, and phospholipase. Furthermore, it was also found that LvS-8n3 exhibits strong pathogenicity, probably due to its high production of pathogenic factors and the ability to utilize nitrite for proliferation. Therefore, the proliferation of pathogenic Photobacterium species appears pivotal for driving shrimp mortality caused by nitrite exposure. These findings provide novel insights into the disease mechanism in shrimp under conditions of environmental change.
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Affiliation(s)
- Yongming Wang
- MOE Key Laboratory of Marine Genetics & Breeding and College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics & Breeding and College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Yue Sun
- MOE Key Laboratory of Marine Genetics & Breeding and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics & Breeding and College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Weipeng Zhang
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics & Breeding and College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics & Breeding and College of Marine Life Sciences, Ocean University of China, Qingdao, China.
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14
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Jiang F, Hao X, Li D, Zhu X, Huang J, Lai Q, Wang J, Wang L, Shao Z. Aquibium pacificus sp. nov., a Novel Mixotrophic Bacterium from Bathypelagic Seawater in the Western Pacific Ocean. Microorganisms 2024; 12:1584. [PMID: 39203426 PMCID: PMC11356281 DOI: 10.3390/microorganisms12081584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 07/28/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
A novel Gram-stain-negative, facultatively anaerobic, and mixotrophic bacterium, designated as strain LZ166T, was isolated from the bathypelagic seawater in the western Pacific Ocean. The cells were short rod-shaped, oxidase- and catalase-positive, and motile by means of lateral flagella. The growth of strain LZ166T was observed at 10-45 °C (optimum 34-37 °C), at pH 5-10 (optimum 6-8), and in the presence of 0-5% NaCl (optimum 1-3%). A phylogenetic analysis based on the 16S rRNA gene showed that strain LZ166T shared the highest similarity (98.58%) with Aquibium oceanicum B7T and formed a distinct branch within the Aquibium genus. The genomic characterization, including average nucleotide identity (ANI, 90.73-76.79%), average amino identity (AAI, 88.50-79.03%), and digital DNA-DNA hybridization (dDDH, 36.1-22.2%) values between LZ166T and other species within the Aquibium genus, further substantiated its novelty. The genome of strain LZ166T was 6,119,659 bp in size with a 64.7 mol% DNA G+C content. The predominant fatty acid was summed feature 8 (C18:1ω7c and/or C18:1ω6c). The major polar lipids identified were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), glycolipid (GL), and phosphatidylglycerol (PG), with ubiquinone-10 (Q-10) as the predominant respiratory quinone. The genomic annotation indicated the presence of genes for a diverse metabolic profile, including pathways for carbon fixation via the Calvin-Benson-Bassham cycle and inorganic sulfur oxidation. Based on the polyphasic taxonomic results, strain LZ166T represented a novel species of the genus Aquibium, for which the name Aquibium pacificus sp. nov. is proposed, with the type strain LZ166T (=MCCC M28807T = KACC 23148T = KCTC 82889T).
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Affiliation(s)
- Fan Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xun Hao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Ding Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Xuying Zhu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Jiamei Huang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Jianning Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Liping Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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15
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De Filippis F, Valentino V, Yap M, Cabrera-Rubio R, Barcenilla C, Carlino N, Cobo-Díaz JF, Quijada NM, Calvete-Torre I, Ruas-Madiedo P, Sabater C, Sequino G, Pasolli E, Wagner M, Margolles A, Segata N, Álvarez-Ordóñez A, Cotter PD, Ercolini D. Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities. NPJ Biofilms Microbiomes 2024; 10:67. [PMID: 39095404 PMCID: PMC11297241 DOI: 10.1038/s41522-024-00541-5] [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: 03/19/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
The resident microbiome in food industries may impact on food quality and safety. In particular, microbes residing on surfaces in dairy industries may actively participate in cheese fermentation and ripening and contribute to the typical flavor and texture. In this work, we carried out an extensive microbiome mapping in 73 cheese-making industries producing different types of cheeses (fresh, medium and long ripened) and located in 4 European countries. We sequenced and analyzed metagenomes from cheese samples, raw materials and environmental swabs collected from both food contact and non-food contact surfaces, as well as operators' hands and aprons. Dairy plants were shown to harbor a very complex microbiome, characterized by high prevalence of genes potentially involved in flavor development, probiotic activities, and resistance to gastro-intestinal transit, suggesting that these microbes may potentially be transferred to the human gut microbiome. More than 6100 high-quality Metagenome Assembled Genomes (MAGs) were reconstructed, including MAGs from several Lactic Acid Bacteria species and putative new species. Although microbial pathogens were not prevalent, we found several MAGs harboring genes related to antibiotic resistance, highlighting that dairy industry surfaces represent a potential hotspot for antimicrobial resistance (AR) spreading along the food chain. Finally, we identified facility-specific strains that can represent clear microbial signatures of different cheesemaking facilities, suggesting an interesting potential of microbiome tracking for the traceability of cheese origin.
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Affiliation(s)
- Francesca De Filippis
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, NA, Italy
| | - Vincenzo Valentino
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
| | - Min Yap
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna, Spain
| | - Coral Barcenilla
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | | | - José F Cobo-Díaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Narciso Martín Quijada
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Inés Calvete-Torre
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Giuseppina Sequino
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
| | - Edoardo Pasolli
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, NA, Italy
| | - Martin Wagner
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Danilo Ercolini
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, NA, Italy.
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16
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Gao Y, Zhang W, Zhang T, Yu Y, Mao S, Liu J. Fructo-oligosaccharide supplementation enhances the growth of nursing dairy calves while stimulating the persistence of Bifidobacterium and hindgut microbiome's maturation. J Dairy Sci 2024; 107:5626-5638. [PMID: 38522831 DOI: 10.3168/jds.2024-24468] [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: 12/05/2023] [Accepted: 02/19/2024] [Indexed: 03/26/2024]
Abstract
The colonization and development of the gut microbiome in dairy calves play a crucial role in their overall health and future productivity. Despite the widely proposed benefits of inulin-related products on the host, there is insufficient information about how supplementing fructo-oligosaccharides (FOS) affects the colonization and development of the gut microbiome in calves. In a randomized intervention trial involving newborn male Holstein dairy calves, we investigated the effect of FOS on the calf hindgut microbiome, short-chain fatty acids (SCFA), growth performance, and the incidence of diarrhea. The daily administration of FOS exhibited a time-dependent increase in the ADG and the concentration of SCFA. Concurrently, FOS delayed the natural decline of Bifidobacterium, promoting the maturation and stabilization of the hindgut microbiome. These findings not only contribute to a theoretical understanding of the judicious application of prebiotics but also hold significant practical implications for the design of early life dietary interventions in the rearing of dairy calves.
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Affiliation(s)
- Yunlong Gao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wanqiu Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yueying Yu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinxin Liu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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17
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Glendinning L, Jia X, Kebede A, Oyola SO, Park JE, Park W, Assiri A, Holm JB, Kristiansen K, Han J, Hanotte O. Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia. MICROBIOME 2024; 12:138. [PMID: 39044244 PMCID: PMC11267795 DOI: 10.1186/s40168-024-01847-4] [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: 07/04/2023] [Accepted: 05/28/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies. RESULTS Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database. CONCLUSIONS The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.
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Affiliation(s)
- Laura Glendinning
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK.
| | - Xinzheng Jia
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, People's Republic of China.
| | - Adebabay Kebede
- CTLGH - LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
| | - Samuel O Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Jong-Eun Park
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, 63243, Jeju, Republic of Korea
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, 55365, Wanju, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, 55365, Wanju, Republic of Korea
| | - Abdulwahab Assiri
- School of Life Sciences, the University of Nottingham, University Park, Nottingham, UK
- Department of Animal and Fisheries Production, King Faisal University, Al-Hofuf, Saudi Arabia
| | - Jacob Bak Holm
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Clinical Microbiomics, Copenhagen, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, People's Republic of China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, People's Republic of China
| | - Olivier Hanotte
- CTLGH - LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
- School of Life Sciences, the University of Nottingham, University Park, Nottingham, UK.
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18
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Nanetti E, Scicchitano D, Palladino G, Interino N, Corlatti L, Pedrotti L, Zanetti F, Pagani E, Esposito E, Brambilla A, Grignolio S, Marotti I, Turroni S, Fiori J, Rampelli S, Candela M. The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion. iScience 2024; 27:110194. [PMID: 38989465 PMCID: PMC11233967 DOI: 10.1016/j.isci.2024.110194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/24/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.
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Affiliation(s)
- Enrico Nanetti
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
| | - Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
| | - Nicolò Interino
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Luca Corlatti
- Stelvio National Park, 23032 Bormio, Italy
- University of Freiburg, 79098 Freiburg, Germany
| | | | - Federica Zanetti
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Elena Pagani
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Erika Esposito
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Alice Brambilla
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich (CH), Switzerland
- Centro Studi Fauna Alpina, Parco Nazionale Gran Paradiso, Loc. Degioz 11, 11010 Valsavarenche, Aosta, Italy
| | - Stefano Grignolio
- University of Ferrara, Department of Life Science and Biotechnology, via Borsari 46, I-44121 Ferrara, Italy
| | - Ilaria Marotti
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Jessica Fiori
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
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19
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Pathak A, Marquez M, Stothard P, Chukwujindu C, Su JQ, Zhou Y, Zhou XY, Jagoe CH, Chauhan A. A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential. iScience 2024; 27:110193. [PMID: 38984199 PMCID: PMC11231605 DOI: 10.1016/j.isci.2024.110193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/09/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024] Open
Abstract
Oyster reefs are hotspots of denitrification mediated removal of dissolved nitrogen (N), however, information on their denitrifier microbiota is scarce. Furthermore, in oyster aquaculture, triploids are often preferred over diploids, yet again, microbiome differences between oyster ploidies are unknown. To address these knowledge gaps, farmed diploid and triploid oysters were collected over an annual growth cycle and analyzed using shotgun metagenomics and quantitative microbial elemental cycling (QMEC) techniques. Regardless of ploidy, Psychrobacter genus was abundant, with positive correlations found for genes of central metabolism, DNA metabolism, and carbohydrate metabolism. MAGs (metagenome-assembled genomes) yielded multiple Psychrobacter genomes harboring norB, narH, narI, and nirK denitrification genes, indicating their functional relevance within the eastern oysters. QMEC analysis indicated the predominance of carbon (C) and nitrogen (N) cycling genes, with no discernable patterns between ploidies. Among the N-cycling genes, the nosZII clade was overrepresented, suggesting its role in the eastern oyster's N removal processes.
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Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| | - Mario Marquez
- Texas Sea Grant College Program, 4115 TAMU Eller O&M 306, Texas A&M University, College Station, TX 77843, USA
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, General Services Bldg, Edmonton, AB 2-31 T6G 2H1, Canada
| | - Christian Chukwujindu
- Material & Energy Technology Department, Projects Development Institute, Emene Industrial Layout, Enugu-Nigeria 400104
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yanyan Zhou
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xin-Yuan Zhou
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Charles H. Jagoe
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
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20
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Selma-Royo M, Ricci L, Golzato D, Servais C, Nabinejad A, Armanini F, Asnicar F, Pinto F, Tamburini S, Segata N. Draft genome sequences of multiple bacterial strains isolated from human feces. Microbiol Resour Announc 2024; 13:e0030724. [PMID: 38809053 PMCID: PMC11256798 DOI: 10.1128/mra.00307-24] [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: 03/26/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
Bacterial isolation is necessary for functional and mechanistic analyses, and the increased human microbiome diversity revealed by metagenomic sequencing is expanding the relevant cultivation targets. Here, we report 46 draft genome sequences of bacterial isolates obtained from fecal samples of healthy adults in Trento and Milan (Italy), including strains from seven taxonomically uncharacterized species.
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Affiliation(s)
| | - Liviana Ricci
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Amir Nabinejad
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | | | | | | | - Sabrina Tamburini
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
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21
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Romanenko L, Bystritskaya E, Savicheva Y, Eremeev V, Otstavnykh N, Kurilenko V, Velansky P, Isaeva M. Description and Whole-Genome Sequencing of Mariniflexile litorale sp. nov., Isolated from the Shallow Sediments of the Sea of Japan. Microorganisms 2024; 12:1413. [PMID: 39065181 PMCID: PMC11278836 DOI: 10.3390/microorganisms12071413] [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: 06/07/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
A Gram-negative, aerobic, rod-shaped, non-motile, yellow-pigmented bacterium, KMM 9835T, was isolated from the sediment sample obtained from the Amur Bay of the Sea of Japan seashore, Russia. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences positioned the novel strain KMM 9835T in the genus Mariniflexile as a separate line sharing the highest 16S rRNA gene sequence similarities of 96.6% and 96.2% with Mariniflexile soesokkakense RSSK-9T and Mariniflexile fucanivorans SW5T, respectively, and similarity values of <96% to other recognized Mariniflexile species. The average nucleotide identity and digital DNA-DNA hybridization values between strain KMM 9835T and M. soesokkakense KCTC 32427T, Mariniflexile gromovii KCTC 12570T, M. fucanivorans DSM 18792T, and M. maritimum M5A1MT were 83.0%, 82.5%, 83.4%, and 78.3% and 30.7%, 29.6%, 29.5%, and 24.4%, respectively. The genomic DNA GC content of strain KMM 9835T was 32.5 mol%. The dominant menaquinone was MK-6, and the major fatty acids were iso-C15:0, iso-C15:1ω10c, and C15:0. The polar lipids of strain KMM 9835T consisted of phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, and six unidentified lipids. A pan-genome analysis showed that the KMM 9835T genome encoded 753 singletons. The annotated singletons were more often related to transport protein systems (SusC), transcriptional regulators (AraC, LytTR, LacI), and enzymes (glycosylases). The KMM 9835T genome was highly enriched in CAZyme-encoding genes, the proportion of which reached 7.3%. Moreover, the KMM 9835T genome was characterized by a high abundance of CAZyme gene families (GH43, GH28, PL1, PL10, CE8, and CE12), indicating its potential to catabolize pectin. This may represent part of an adaptation strategy facilitating microbial consumption of plant polymeric substrates in aquatic environments near shorelines and freshwater sources. Based on the combination of phylogenetic and phenotypic characterization, the marine sediment strain KMM 9835T (=KCTC 92792T) represents a novel species of the genus Mariniflexile, for which the name Mariniflexile litorale sp. nov. is proposed.
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Affiliation(s)
- Lyudmila Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Evgeniya Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Yuliya Savicheva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Viacheslav Eremeev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Nadezhda Otstavnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Valeriya Kurilenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Peter Velansky
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia;
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
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22
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Kumar P, Verma A, Yadav P, Das J, Kumar L, Krishnamurthi S. Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:172995. [PMID: 38719044 DOI: 10.1016/j.scitotenv.2024.172995] [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: 12/14/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537T (96.3 %), H. alexandrii LZ-16-2T (96.2 %) and Parahaliea maris HSLHS9T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164T = MTCC 12907T = KCTC 52755T = JCM 32136T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932T = KCTC 23430T = S1-72T) to Pseudhalioglobus pacificus comb. nov. is also proposed.
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Affiliation(s)
- Pravin Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India; Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden; Umeå Marine Sciences Centre, Hörnefors, Sweden
| | - Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Lalit Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India.
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23
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Huang Y, Xu W, Dong W, Chen G, Sun Y, Zeng X. Anti-diabetic effect of dicaffeoylquinic acids is associated with the modulation of gut microbiota and bile acid metabolism. J Adv Res 2024:S2090-1232(24)00264-9. [PMID: 38969095 DOI: 10.1016/j.jare.2024.06.027] [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: 03/30/2024] [Revised: 06/06/2024] [Accepted: 06/30/2024] [Indexed: 07/07/2024] Open
Abstract
INTRODUCTION The human gut microbiome plays a pivotal role in health and disease, notably through its interaction with bile acids (BAs). BAs, synthesized in the liver, undergo transformation by the gut microbiota upon excretion into the intestine, thus influencing host metabolism. However, the potential mechanisms of dicaffeoylquinic acids (DiCQAs) from Ilex kudingcha how to modulate lipid metabolism and inflammation via gut microbiota remain unclear. OBJECTIVES AND METHODS The objectives of the present study were to investigate the regulating effects of DiCQAs on diabetes and the potential mechanisms of action. Two mice models were utilized to investigate the anti-diabetic effects of DiCQAs. Additionally, analysis of gut microbiota structure and functions was conducted concurrently with the examination of DiCQAs' impact on gut microbiota carrying the bile salt hydrolase (BSH) gene, as well as on the enterohepatic circulation of BAs and related signaling pathways. RESULTS Our findings demonstrated that DiCQAs alleviated diabetic symptoms by modulating gut microbiota carrying the BSH gene. This modulation enhanced intestinal barrier integrity, increased enterohepatic circulation of conjugated BAs, and inhibited the farnesoid X receptor-fibroblast growth factor 15 (FGF15) signaling axis in the ileum. Consequently, the protein expression of hepatic FGFR4 fibroblast growth factor receptor 4 (FGFR4) decreased, accompanied by heightened BA synthesis, reduced hepatic BA stasis, and lowered levels of hepatic and plasma cholesterol. Furthermore, DiCQAs upregulated glucolipid metabolism-related proteins in the liver and muscle, including v-akt murine thymoma viral oncogene homolog (AKT)/glycogen synthase kinase 3-beta (GSK3β) and AMP-activated protein kinase (AMPK), thereby ameliorating hyperglycemia and mitigating inflammation through the down-regulation of the MAPK signaling pathway in the diabetic group. CONCLUSION Our study elucidated the anti-diabetic effects and mechanism of DiCQAs from I. kudingcha, highlighting the potential of targeting gut microbiota, particularly Acetatifactor sp011959105 and Acetatifactor muris carrying the BSH gene, as a therapeutic strategy to attenuate FXR-FGF15 signaling and ameliorate diabetes.
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Affiliation(s)
- Yujie Huang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Weiqi Xu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Wei Dong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Guijie Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yi Sun
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xiaoxiong Zeng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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24
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Shen L, Hu J, Zhang L, Wu Z, Chen L, Adhikari NP, Ji M, Chen S, Peng F, Liu Y. Genomics-based identification of a cold adapted clade in Deinococcus. BMC Biol 2024; 22:145. [PMID: 38956546 PMCID: PMC11218099 DOI: 10.1186/s12915-024-01944-8] [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: 12/27/2023] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Microbes in the cold polar and alpine environments play a critical role in feedbacks that amplify the effects of climate change. Defining the cold adapted ecotype is one of the prerequisites for understanding the response of polar and alpine microbes to climate change. RESULTS Here, we analysed 85 high-quality, de-duplicated genomes of Deinococcus, which can survive in a variety of harsh environments. By leveraging genomic and phenotypic traits with reverse ecology, we defined a cold adapted clade from eight Deinococcus strains isolated from Arctic, Antarctic and high alpine environments. Genome-wide optimization in amino acid composition and regulation and signalling enable the cold adapted clade to produce CO2 from organic matter and boost the bioavailability of mineral nitrogen. CONCLUSIONS Based primarily on in silico genomic analysis, we defined a potential cold adapted clade in Deinococcus and provided an updated view of the genomic traits and metabolic potential of Deinococcus. Our study would facilitate the understanding of microbial processes in the cold polar and alpine environments.
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Affiliation(s)
- Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, and Auhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, Anhui Normal University, Wuhu, 241000, China.
| | - Jiayu Hu
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Luyao Zhang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Zirui Wu
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Liangzhong Chen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Namita Paudel Adhikari
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
| | - Shaoxing Chen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
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25
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Kawamoto H, Watanabe M, Mochimaru H, Nakahara N, Meng XY, Sakamoto S, Morinaga K, Katayama T, Yoshioka H, Nomura N, Tamaki H. Atrimonas thermophila gen. nov., sp. nov., a novel anaerobic thermophilic bacterium of the phylum Atribacterota isolated from deep subsurface gas field and proposal of Atrimonadaceae fam. nov. within the class Atribacteria in the phylum Atribacterota. Syst Appl Microbiol 2024; 47:126515. [PMID: 38776610 DOI: 10.1016/j.syapm.2024.126515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 04/08/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
A novel anaerobic, thermophilic bacterium of the class Atribacteria, strain M15T, was isolated from a high-temperature gas reservoir, Japan. Cells of strain M15T were gram-negative, short oval-shaped, and lacked flagella. Growth occurred at 45-75 °C (optimum 70-75 °C) and pH 6.5-8.5 (optimum pH 7.5-8.0) and was fast under optimal conditions (doubling time 11.4 h). Yeast extract was required for growth. Fermentative growth with glucose, arabinose, xylose, and cellobiose was observed. The major fermentative end products of glucose were acetate and hydrogen. The major cellular fatty acids were C16:0, iso-C15:0, and C18:0. The genomic G + C content was 46.0 mol%. Fluorescence and electron microscopy observations revealed the intracellular localization of genomic DNA surrounded by a membrane in the cells of strain M15T as reported in a sole validly described species of the class Atribacteria in the phylum Atribacterota, Atribacter laminatus strain RT761T, suggesting that the unique morphological traits are widely shared in this class. Phylogenetic analyses indicated that strain M15T belongs to a distinct family-level lineage in the class Atribacteria and shows low similarities to Atribacter laminatus strain RT761T (16S rRNA gene sequence identity of 90.1 %, average nucleotide identity [ANI] of 66.1 %, average amino acid identity [AAI] of 55.8 %). Phenotypic traits of strain M15T (thermophilic, fast-growing, relatively high G + C content, etc.) were clearly distinct from A. laminatus. Based on these phenotypic and genomic properties, we propose a novel genus and species, Atrimonas thermophila gen. nov., sp. nov. for strain M15T (=JCM39389T, =KCTC25731T) representing a novel family Atrimonadaceae fam., nov. in the class Atribacteria.
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Affiliation(s)
- Hiroki Kawamoto
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Miho Watanabe
- Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, Shimo-Shinjyo Nakano, Akita 010-0195, Japan
| | - Hanako Mochimaru
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Nozomi Nakahara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan; Environmental Management Center, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Xiang-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Sachiko Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Taiki Katayama
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hideyoshi Yoshioka
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; MiCS (Microbiology Research Center for Sustainability), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; MiCS (Microbiology Research Center for Sustainability), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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26
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Jia M, Zhu S, Xue MY, Chen H, Xu J, Song M, Tang Y, Liu X, Tao Y, Zhang T, Liu JX, Wang Y, Sun HZ. Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome. Nat Microbiol 2024; 9:1884-1898. [PMID: 38866938 DOI: 10.1038/s41564-024-01723-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem.
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Affiliation(s)
- Minghui Jia
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Senlin Zhu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Ming-Yuan Xue
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Xianghu Laboratory, Hangzhou, China
| | - Hongyi Chen
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Jinghong Xu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Mengdi Song
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- M20 Genomics, Hangzhou, China
| | - Yifan Tang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Xiaohan Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Ye Tao
- Shanghai Biozeron Biotechnology Company, Shanghai, China
| | - Tianyu Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- M20 Genomics, Hangzhou, China
| | - Jian-Xin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Yongcheng Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Hui-Zeng Sun
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China.
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China.
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27
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Videau P, Shlafstein MD, Oline DK, Givan SA, Chapman LF, Strangman WK, Hahnke RL, Saw JH, Ushijima B. Genome-based taxonomic analysis of the genus Pseudoalteromonas reveals heterotypic synonyms. Environ Microbiol 2024; 26:e16672. [PMID: 39040020 DOI: 10.1111/1462-2920.16672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/31/2024] [Indexed: 07/24/2024]
Abstract
The Pseudoalteromonas genus comprises members that have been demonstrated to play significant ecological roles and produce enzymes, natural products, and activities that are beneficial to the environment and economy. A comprehensive evaluation of the genus revealed that the genomes of several Pseudoalteromonas species are highly similar to each other, exceeding species cutoff values. This evaluation involved determining and comparing the average nucleotide identity, in silico DNA-DNA hybridization, average amino acid identity, and the difference in G + C% between Pseudoalteromonas type strains with publicly available genomes. The genome of the Pseudoalteromonas elyakovii type strain was further assessed through additional sequencing and genomic comparisons to historical sequences. These findings suggest that six Pseudoalteromonas species, namely P. mariniglutinosa, P. donghaensis, P. maricaloris, P. elyakovii, P. profundi, and P. issachenkonii, should be reclassified as later heterotypic synonyms of the following validly published species: P. haloplanktis, P. lipolytica, P. flavipulchra, P. distincta, P. gelatinilytica, and P. tetraodonis. Furthermore, two names without valid standing, 'P. telluritireducens' and 'P. spiralis', should be associated with the validly published Pseudoalteromonas species P. agarivorans and P. tetraodonis, respectively.
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Affiliation(s)
- Patrick Videau
- Department of Biology, Southern Oregon University, Ashland, Oregon, USA
| | | | - David K Oline
- Department of Biology, Southern Oregon University, Ashland, Oregon, USA
| | - Scott A Givan
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Linda Fleet Chapman
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Wendy K Strangman
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Richard L Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jimmy H Saw
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
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28
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Banerjee G, Papri SR, Banerjee P. Protocol for the construction and functional profiling of metagenome-assembled genomes for microbiome analyses. STAR Protoc 2024; 5:103167. [PMID: 38954516 PMCID: PMC11263634 DOI: 10.1016/j.xpro.2024.103167] [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: 03/25/2024] [Revised: 05/08/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Constructing metagenome-assembled genomes (MAGs) from complex metagenomic samples involves a series of bioinformatics operations, each requiring deep bioinformatics knowledge. Here, we present a protocol for constructing MAGs and conducting functional profiling to address biological questions. We describe steps for system configuration, data downloads, read processing, removal of human DNA contamination, metagenomic assembly, and statistical quality assessment of the final assembly. Additionally, we detail procedures for the construction and refinement of MAGs, as well as the functional profiling of MAGs.
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Affiliation(s)
- Goutam Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Suraya Rahman Papri
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pratik Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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29
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Teichman S, Lee MD, Willis AD. Analyzing microbial evolution through gene and genome phylogenies. Biostatistics 2024; 25:786-800. [PMID: 37897441 PMCID: PMC11247178 DOI: 10.1093/biostatistics/kxad025] [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: 02/10/2023] [Revised: 08/15/2023] [Accepted: 08/27/2023] [Indexed: 10/30/2023] Open
Abstract
Microbiome scientists critically need modern tools to explore and analyze microbial evolution. Often this involves studying the evolution of microbial genomes as a whole. However, different genes in a single genome can be subject to different evolutionary pressures, which can result in distinct gene-level evolutionary histories. To address this challenge, we propose to treat estimated gene-level phylogenies as data objects, and present an interactive method for the analysis of a collection of gene phylogenies. We use a local linear approximation of phylogenetic tree space to visualize estimated gene trees as points in low-dimensional Euclidean space, and address important practical limitations of existing related approaches, allowing an intuitive visualization of complex data objects. We demonstrate the utility of our proposed approach through microbial data analyses, including by identifying outlying gene histories in strains of Prevotella, and by contrasting Streptococcus phylogenies estimated using different gene sets. Our method is available as an open-source R package, and assists with estimating, visualizing, and interacting with a collection of bacterial gene phylogenies.
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Affiliation(s)
- Sarah Teichman
- University of Washington Department of Statistics, Box 354322, Seattle, WA 98195-4322, USA
| | - Michael D Lee
- KBR NASA Ames Research Center, PO Box 1, Moffett Field, CA 94035-1000
- Blue Marble Space Institute of Science, 600 1st Avenue, 1st Floor, Seattle, WA 98104, USA
| | - Amy D Willis
- University of Washington Department of Biostatistics, Hans Rosling Center for Population Health, Box 351617, Seattle, WA 98195-1617, USA
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30
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Song K, Wang S, Xu X, Ma J, Yang Y, Zeng Y, Li J, Zhou X, Zhou Y. Benthic clade II-type nitrous oxide reducers suppress nitrous oxide emissions in shallow lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172908. [PMID: 38697552 DOI: 10.1016/j.scitotenv.2024.172908] [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: 02/22/2024] [Revised: 04/07/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Shallow lakes, recognized as hotspots for nitrogen cycling, contribute to the emission of the potent greenhouse gas nitrous oxide (N2O), but the current emission estimates for this gas have a high degree of uncertainty. However, the role of N2O-reducing bacteria (N2ORB) as N2O sinks and their contribution to N2O reduction in aquatic ecosystems in response to N2O dynamics have not been determined. Here, we investigated the N2O dynamics and microbial processes in the nitrogen cycle, which included both N2O production and consumption, in five shallow lakes spanning approximately 500 km. The investigated sites exhibited N2O oversaturation, with excess dissolved N2O concentrations (ΔN2O) ranging from 0.55 ± 0.61 to 53.17 ± 15.75 nM. Sediment-bound N2O (sN2O) was significantly positively correlated with the nitrate concentration in the overlying water (p < 0.05), suggesting that nitrate accumulation contributes to benthic N2O generation. High N2O consumption activity (RN2O) corresponded to low ΔN2O. In addition, a significant negative correlation was found between RN2O and nir/nosZ, showing that bacteria encoding nosZ contributed to N2O consumption in the benthic sediments. Redundancy analysis indicated that benthic functional genes effectively reflected the variations in RN2O and ∆N2O. qPCR analysis revealed that the clade II nosZ gene was more sensitive to ΔN2O than the clade I nosZ gene. Furthermore, four novel genera of potential nondenitrifying N2ORB were identified based on metagenome-assembled genome analysis. These genera, which are affiliated with clade II, lack genes responsible for N2O production. Collectively, benthic N2ORB, especially for clade II-type N2ORB, harnesses N2O consumption activity leading to low N2O emissions from shallow lakes. This study advances our knowledge of the role of benthic clade II-type N2ORB in regulating N2O emissions in shallow lakes.
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Affiliation(s)
- Kang Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaoguang Xu
- School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Jie Ma
- Ministry of Ecology and Environment, Nanjing Institute of Environment Sciences, Nanjing 210042, China
| | - Yuxuan Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Yuli Zeng
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jining Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaohong Zhou
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yiwen Zhou
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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31
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Cueva-Yesquén LG, Sartoratto A, da Silva Santos A, de Melo IS, Fantinatti-Garboggini F. Pseudomonas flavocrustae sp. nov., an endophyte with plant growth promoting traits isolated from Passiflora incarnata. Sci Rep 2024; 14:14285. [PMID: 38902258 PMCID: PMC11190252 DOI: 10.1038/s41598-024-64349-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
A polyphasic approach was applied to characterize taxonomically a novel endophytic bacterial strain, designated as EP178T, which was previously isolated from Passiflora incarnata leaves and characterized as plant-growth promoter. The strain EP178T forms Gram stain-negative and rod-shaped cells, and circular and yellow-pigmented colonies. Its growth occurs at 10-37 °C, at pH 6.0-8.0, and tolerates up to 7% (w/v) NaCl. The major cellular fatty acids found were summed feature 8 (C18:1 ω7c), summed feature 3 (C16:1 ω6c /C16:1 ω7c), and C16:0, and the predominant ubiquinone was Q-9. The phylogenetic and nucleotide-similarity analysis with 16S rRNA gene sequences showed that strain EP178T belongs to Pseudomonas genus. The genomic-based G + C content was 65.5%. The average nucleotide identity and digital DNA-DNA hybridization values between strains EP178T and the closest type strain, P. oryzihabitans DSM 6835T, were 92.6% and 52.2%, respectively. Various genes associated with plant-growth promoting mechanisms were annotated from genome sequences. Based on the phenotypic, genomic, phylogeny and chemotaxonomic data, strain EP178T represents a new species of the genus Pseudomonas, for which the name Pseudomonas flavocrustae sp. nov. was proposed. The type strain is EP178T (= CBMAI 2609T = ICMP 24844T = MUM 23.01T).
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Affiliation(s)
- Luis Gabriel Cueva-Yesquén
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.
- Division of Microbial Resources, Research Center for Agriculture, Biological and Chemical, University of Campinas, Paulínia, SP, Brazil.
| | - Adilson Sartoratto
- Division of Organic and Pharmaceutical Chemical, Research Center for Agriculture, Biological and Chemical, University of Campinas, Paulínia, SP, Brazil
| | - Adriana da Silva Santos
- Division of Organic and Pharmaceutical Chemical, Research Center for Agriculture, Biological and Chemical, University of Campinas, Paulínia, SP, Brazil
| | - Itamar Soares de Melo
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, Jaguariúna, SP, CEP 13820-000, Brazil
| | - Fabiana Fantinatti-Garboggini
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.
- Division of Microbial Resources, Research Center for Agriculture, Biological and Chemical, University of Campinas, Paulínia, SP, Brazil.
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Hu WF, Yang JY, Wang JJ, Yuan SF, Yue XJ, Zhang Z, Zhang YQ, Meng JY, Li YZ. Characteristics and immune functions of the endogenous CRISPR-Cas systems in myxobacteria. mSystems 2024; 9:e0121023. [PMID: 38747603 PMCID: PMC11237760 DOI: 10.1128/msystems.01210-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/15/2024] [Indexed: 06/19/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) system widely occurs in prokaryotic organisms to recognize and destruct genetic invaders. Systematic collation and characterization of endogenous CRISPR-Cas systems are conducive to our understanding and potential utilization of this natural genetic machinery. In this study, we screened 39 complete and 692 incomplete genomes of myxobacteria using a combined strategy to dispose of the abridged genome information and revealed at least 19 CRISPR-Cas subtypes, which were distributed with a taxonomic difference and often lost stochastically in intraspecies strains. The cas genes in each subtype were evolutionarily clustered but deeply separated, while most of the CRISPRs were divided into four types based on the motif characteristics of repeat sequences. The spacers recorded in myxobacterial CRISPRs were in high G+C content, matching lots of phages, tiny amounts of plasmids, and, surprisingly, massive organismic genomes. We experimentally demonstrated the immune and self-target immune activities of three endogenous systems in Myxococcus xanthus DK1622 against artificial genetic invaders and revealed the microhomology-mediated end-joining mechanism for the immunity-induced DNA repair but not homology-directed repair. The panoramic view and immune activities imply potential omnipotent immune functions and applications of the endogenous CRISPR-Cas machinery. IMPORTANCE Serving as an adaptive immune system, clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) empower prokaryotes to fend off the intrusion of external genetic materials. Myxobacteria are a collective of swarming Gram-stain-negative predatory bacteria distinguished by intricate multicellular social behavior. An in-depth analysis of their intrinsic CRISPR-Cas systems is beneficial for our understanding of the survival strategies employed by host cells within their environmental niches. Moreover, the experimental findings presented in this study not only suggest the robust immune functions of CRISPR-Cas in myxobacteria but also their potential applications.
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Affiliation(s)
- Wei-Feng Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jiang-Yu Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Shu-Fei Yuan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Ya-Qi Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jun-Yan Meng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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Yadegar A, Bar-Yoseph H, Monaghan TM, Pakpour S, Severino A, Kuijper EJ, Smits WK, Terveer EM, Neupane S, Nabavi-Rad A, Sadeghi J, Cammarota G, Ianiro G, Nap-Hill E, Leung D, Wong K, Kao D. Fecal microbiota transplantation: current challenges and future landscapes. Clin Microbiol Rev 2024; 37:e0006022. [PMID: 38717124 PMCID: PMC11325845 DOI: 10.1128/cmr.00060-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
SUMMARYGiven the importance of gut microbial homeostasis in maintaining health, there has been considerable interest in developing innovative therapeutic strategies for restoring gut microbiota. One such approach, fecal microbiota transplantation (FMT), is the main "whole gut microbiome replacement" strategy and has been integrated into clinical practice guidelines for treating recurrent Clostridioides difficile infection (rCDI). Furthermore, the potential application of FMT in other indications such as inflammatory bowel disease (IBD), metabolic syndrome, and solid tumor malignancies is an area of intense interest and active research. However, the complex and variable nature of FMT makes it challenging to address its precise functionality and to assess clinical efficacy and safety in different disease contexts. In this review, we outline clinical applications, efficacy, durability, and safety of FMT and provide a comprehensive assessment of its procedural and administration aspects. The clinical applications of FMT in children and cancer immunotherapy are also described. We focus on data from human studies in IBD in contrast with rCDI to delineate the putative mechanisms of this treatment in IBD as a model, including colonization resistance and functional restoration through bacterial engraftment, modulating effects of virome/phageome, gut metabolome and host interactions, and immunoregulatory actions of FMT. Furthermore, we comprehensively review omics technologies, metagenomic approaches, and bioinformatics pipelines to characterize complex microbial communities and discuss their limitations. FMT regulatory challenges, ethical considerations, and pharmacomicrobiomics are also highlighted to shed light on future development of tailored microbiome-based therapeutics.
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Affiliation(s)
- Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Haggai Bar-Yoseph
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tanya Marie Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Sepideh Pakpour
- School of Engineering, Faculty of Applied Sciences, UBC, Okanagan Campus, Kelowna, British Columbia, Canada
| | - Andrea Severino
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Ed J Kuijper
- Center for Microbiota Analysis and Therapeutics (CMAT), Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Wiep Klaas Smits
- Center for Microbiota Analysis and Therapeutics (CMAT), Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Elisabeth M Terveer
- Center for Microbiota Analysis and Therapeutics (CMAT), Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Sukanya Neupane
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Sadeghi
- School of Engineering, Faculty of Applied Sciences, UBC, Okanagan Campus, Kelowna, British Columbia, Canada
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Estello Nap-Hill
- Department of Medicine, Division of Gastroenterology, St Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dickson Leung
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Karen Wong
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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Lukovic B, Kabic J, Dragicevic M, Kuljanin S, Dimkic I, Jovcic B, Gajic I. Genetic basis of antimicrobial resistance, virulence features and phylogenomics of carbapenem-resistant Acinetobacter baumannii clinical isolates. Infection 2024:10.1007/s15010-024-02316-8. [PMID: 38856809 DOI: 10.1007/s15010-024-02316-8] [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: 03/06/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
PURPOSE The worldwide emergence and clonal spread of carbapenem-resistant Acinetobacter baumannii (CRAB) is of great concern. In the present study, we determined the mechanisms of antimicrobial resistance, virulence gene repertoire and genomic relatedness of CRAB isolates circulating in Serbian hospitals. METHODS CRAB isolates were analyzed using whole-genome sequencing (WGS) for the presence of antimicrobial resistance-encoding genes, virulence factors-encoding genes, mobile genetic elements and genomic relatedness. Antimicrobial susceptibility testing was done by disk diffusion and broth microdilution methods. RESULTS Eleven isolates exhibited an MDR resistance phenotype, while four of them were XDR. MIC90 for meropenem and imipenem were > 64 µg/mL and 32 µg/mL, respectively. While all CRABs harbored blaOXA-66 variant of blaOXA-51 gene, those assigned to STPas2, STPas636 and STPas492 had blaADC-73,blaADC-74 and blaADC-30 variants, respectively. The following acquired carbapenemases-encoding genes were found: blaOXA-72 (n = 12), blaOXA-23 (n = 3), and blaNDM-1(n = 5), and were mapped to defined mobile genetic elements. MLST analysis assigned the analyzed CRAB isolates to three Pasteur sequence types (STs): STPas2, STPas492, and STPas636. The Majority of strains belonged to International Clone II (ICII) and carried tested virulence-related genes liable for adherence, biofilm formation, iron uptake, heme biosynthesis, zinc utilization, serum resistance, stress adaptation, intracellular survival and toxin activity. CONCLUSION WGS elucidated the resistance and virulence profiles of CRABs isolated from clinical samples in Serbian hospitals and genomic relatedness of CRAB isolates from Serbia and globally distributed CRABs.
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Affiliation(s)
- Bojana Lukovic
- College of Health Sciences, Academy of Applied Studies Belgrade, Cara Dusana 254, Belgrade, 11080, Serbia.
| | - Jovana Kabic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Milan Dragicevic
- Institute for Biological Research "Siniša Stanković", National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Ivica Dimkic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Branko Jovcic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Ina Gajic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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Jiang Y, McDonald D, Perry D, Knight R, Mirarab S. Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. Bioinformatics 2024; 40:btae361. [PMID: 38870525 PMCID: PMC11193062 DOI: 10.1093/bioinformatics/btae361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 04/09/2024] [Accepted: 06/12/2024] [Indexed: 06/15/2024] Open
Abstract
MOTIVATION Phylogenetic placement of a query sequence on a backbone tree is increasingly used across biomedical sciences to identify the content of a sample from its DNA content. The accuracy of such analyses depends on the density of the backbone tree, making it crucial that placement methods scale to very large trees. Moreover, a new paradigm has been recently proposed to place sequences on the species tree using single-gene data. The goal is to better characterize the samples and to enable combined analyses of marker-gene (e.g., 16S rRNA gene amplicon) and genome-wide data. The recent method DEPP enables performing such analyses using metric learning. However, metric learning is hampered by a need to compute and save a quadratically growing matrix of pairwise distances during training. Thus, the training phase of DEPP does not scale to more than roughly 10 000 backbone species, a problem that we faced when trying to use our recently released Greengenes2 (GG2) reference tree containing 331 270 species. RESULTS This paper explores divide-and-conquer for training ensembles of DEPP models, culminating in a method called C-DEPP. While divide-and-conquer has been extensively used in phylogenetics, applying divide-and-conquer to data-hungry machine-learning methods needs nuance. C-DEPP uses carefully crafted techniques to enable quasi-linear scaling while maintaining accuracy. C-DEPP enables placing 20 million 16S fragments on the GG2 reference tree in 41 h of computation. AVAILABILITY AND IMPLEMENTATION The dataset and C-DEPP software are freely available at https://github.com/yueyujiang/dataset_cdepp/.
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Affiliation(s)
- Yueyu Jiang
- Electrical and Computer Engineering Department, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
| | - Daniel McDonald
- Pediatrics Department, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
| | - Daniela Perry
- Pediatrics Department, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
| | - Rob Knight
- Pediatrics Department, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
| | - Siavash Mirarab
- Electrical and Computer Engineering Department, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
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Wang S, Nie W, Gu Q, Wang X, Yang D, Li H, Wang P, Liao W, Huang J, Yuan Q, Zhou S, Ahmad I, Kotaro K, Chen G, Zhu B. Spread of antibiotic resistance genes in drinking water reservoirs: Insights from a deep metagenomic study using a curated database. WATER RESEARCH 2024; 256:121572. [PMID: 38621316 DOI: 10.1016/j.watres.2024.121572] [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: 01/05/2024] [Revised: 03/13/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
The exploration of antibiotic resistance genes (ARGs) in drinking water reservoirs is an emerging field. Using a curated database, we enhanced the ARG detection and conducted a comprehensive analysis using 2.2 Tb of deep metagenomic sequencing data to determine the distribution of ARGs across 16 drinking water reservoirs and associated environments. Our findings reveal a greater diversity of ARGs in sediments than in water, underscoring the importance of extensive background surveys. Crucial ARG carriers-specifically Acinetobacter, Pseudomonas, and Mycobacterium were identified in drinking water reservoirs. Extensive analysis of the data uncovered a considerable concern for drinking water safety, particularly in regions reliant on river sources. Mobile genetic elements have been found to contribute markedly to the propagation of ARGs. The results of this research suggest that the establishment of drinking water reservoirs for supplying raw water may be an effective strategy for alleviating the spread of water-mediated ARGs.
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Affiliation(s)
- Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenhan Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
| | - Qing Gu
- Zhejiang Province Ecological and Environmental Monitoring Centre, Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Hangzhou, 310012, China
| | - Xie Wang
- Southwest China Mountain Agricultural Environment Key Laboratory, Ministry of Agriculture and Rural Areas, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Shizishan Rd, Chengdu, 610066, China
| | - Danping Yang
- Observation and Research Station of Ecological Restoration for Chongqing Typical Mining Areas, Ministry of Natural Resources (Chongqing Institute of Geology and Mineral Resources), Chongqing, 401120. China
| | - Hongyu Li
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peihong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weixue Liao
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Huang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Quan Yuan
- School of Energy and Power Engineering, Xihua University, Chengdu, 610039, China
| | - Shengli Zhou
- Zhejiang Province Ecological and Environmental Monitoring Centre, Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Hangzhou, 310012, China
| | - Iftikhar Ahmad
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Kiga Kotaro
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Gongyou Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Chen H, Huang Z. Marortus luteolus Yu et al. 2019 is a later heterotypic synonym of Zhongshania marina On et al. 2019. Int J Syst Evol Microbiol 2024; 74. [PMID: 38888588 DOI: 10.1099/ijsem.0.006431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024] Open
Abstract
Phylogeny of 16S rRNA gene sequences showed that Marortus luteolus ZX-21T and Zhongshania marina DSW25-10T are closely related, and form a monophyletic clade affiliated with the genus Zhongshania. Whole genome sequence comparisons showed that M. luteolus ZX-21T and Z. marina DSW25-10T shared 78.8 % digital DNA-DNA hybridization, 97.6 % average nucleotide identity and 98.1 % average amino acid identity. These values exceeded the recommended threshold values for species delineation. Thus, based on the principle of priority, we propose the reclassification of Marortus luteolus Yu et al. 2019 as a later heterotypic synonym of Zhongshania marina On et al. 2019.
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Affiliation(s)
- Huaiyu Chen
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, PR China
| | - Zhaobin Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, PR China
- Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, Quanzhou, PR China
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Klimek D, Herold M, Calusinska M. Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes. BMC Genomics 2024; 25:523. [PMID: 38802741 PMCID: PMC11131199 DOI: 10.1186/s12864-024-10413-z] [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: 01/26/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Members of the Planctomycetota phylum harbour an outstanding potential for carbohydrate degradation given the abundance and diversity of carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members of the Planctomycetia class have been characterised up to now, and little is known about the degrading capacities of the other Planctomycetota. Here, we present a comprehensive comparative analysis of all available planctomycetotal genome representatives and detail encoded carbohydrolytic potential across phylogenetic groups and different habitats. RESULTS Our in-depth characterisation of the available planctomycetotal genomic resources increases our knowledge of the carbohydrolytic capacities of Planctomycetota. We show that this single phylum encompasses a wide variety of the currently known CAZyme diversity assigned to glycoside hydrolase families and that many members encode a versatile enzymatic machinery towards complex carbohydrate degradation, including lignocellulose. We highlight members of the Isosphaerales, Pirellulales, Sedimentisphaerales and Tepidisphaerales orders as having the highest encoded hydrolytic potential of the Planctomycetota. Furthermore, members of a yet uncultivated group affiliated to the Phycisphaerales order could represent an interesting source of novel lytic polysaccharide monooxygenases to boost lignocellulose degradation. Surprisingly, many Planctomycetota from anaerobic digestion reactors encode CAZymes targeting algal polysaccharides - this opens new perspectives for algal biomass valorisation in biogas processes. CONCLUSIONS Our study provides a new perspective on planctomycetotal carbohydrolytic potential, highlighting distinct phylogenetic groups which could provide a wealth of diverse, potentially novel CAZymes of industrial interest.
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Affiliation(s)
- Dominika Klimek
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg.
- The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, 2 Avenue de l'Université, Esch-sur-Alzette, L-4365, Luxembourg.
| | - Malte Herold
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg
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Meng Y, Zhang X, Zhai Y, Li Y, Shao Z, Liu S, Zhang C, Xing XH, Zheng H. Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis. MICROBIOME 2024; 12:93. [PMID: 38778376 PMCID: PMC11112851 DOI: 10.1186/s40168-024-01813-0] [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: 09/14/2023] [Accepted: 04/09/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND The gut microbiota and their hosts profoundly affect each other's physiology and evolution. Identifying host-selected traits is crucial to understanding the processes that govern the evolving interactions between animals and symbiotic microbes. Current experimental approaches mainly focus on the model bacteria, like hypermutating Escherichia coli or the evolutionary changes of wild stains by host transmissions. A method called atmospheric and room temperature plasma (ARTP) may overcome the bottleneck of low spontaneous mutation rates while maintaining mild conditions for the gut bacteria. RESULTS We established an experimental symbiotic system with gnotobiotic bee models to unravel the molecular mechanisms promoting host colonization. By in vivo serial passage, we tracked the genetic changes of ARTP-treated Snodgrassella strains from Bombus terrestris in the non-native honeybee host. We observed that passaged isolates showing genetic changes in the mutual gliding locus have a competitive advantage in the non-native host. Specifically, alleles in the orphan mglB, the GTPase activating protein, promoted colonization potentially by altering the type IV pili-dependent motility of the cells. Finally, competition assays confirmed that the mutations out-competed the ancestral strain in the non-native honeybee gut but not in the native host. CONCLUSIONS Using the ARTP mutagenesis to generate a mutation library of gut symbionts, we explored the potential genetic mechanisms for improved gut colonization in non-native hosts. Our findings demonstrate the implication of the cell mutual-gliding motility in host association and provide an experimental system for future study on host-microbe interactions. Video Abstract.
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Affiliation(s)
- Yujie Meng
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
- MGI Tech, Qingdao, 266426, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100083, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yuan Li
- MGI Tech, Qingdao, 266426, China
| | | | | | - Chong Zhang
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xin-Hui Xing
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Hao Zheng
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
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Xiao Z, Zhang Y, Zhang W, Zhang A, Wang G, Chen C, Ullah H, Ayaz T, Li S, Zhaxi D, Yan Q, Kang J, Xu X. Characterizations of gut bacteriome, mycobiome, and virome of healthy individuals living in sea-level and high-altitude areas. Int Microbiol 2024:10.1007/s10123-024-00531-9. [PMID: 38758414 DOI: 10.1007/s10123-024-00531-9] [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: 12/27/2023] [Revised: 04/05/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND The contribution of gut microbiota to human high-altitude adaptation remains inadequately understood. METHODS Here a comparative analysis of gut microbiota was conducted between healthy individuals living at sea level and high altitude using deep whole-metagenome shotgun sequencing, to investigate the adaptive mechanisms of gut microbiota in plateau inhabitants. RESULTS The results showed the gut bacteriomes in high-altitude individuals exhibited greater within-sample diversity and significant alterations in both bacterial compositional and functional profiles when compared to those of sea-level individuals, indicating the potential selection of unique bacteria associated with high-altitude environments. The strain-level investigation revealed enrichment of Collinsella aerofaciens and Akkermansia muciniphila in high-altitude populations. The characteristics of gut virome and gut mycobiome were also investigated. Compared to sea-level subjects, high-altitude subjects exhibited a greater diversity in their gut virome, with an increased number of viral operational taxonomic units (vOTUs) and unique annotated genes. Finally, correlation analyses revealed 819 significant correlations between 42 bacterial species and 375 vOTUs, while no significant correlations were observed between bacteria and fungi or between fungi and viruses. CONCLUSION The findings have significantly contributed to an enhanced comprehension of the mechanisms underlying the high-altitude geographic adaptation of the human gut microbiota.
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Affiliation(s)
- Zhen Xiao
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, 430010, China
| | - Wei Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Aiqin Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550003, China
| | - Hayan Ullah
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Taj Ayaz
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430010, China
| | - Duoji Zhaxi
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Jian Kang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Xiaoguang Xu
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China.
- Department of Neurosurgery, Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China.
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Wang Y, Zhai J, Tang B, Dong Y, Sun S, He S, Zhao W, Lancuo Z, Jia Q, Wang W. Metagenomic comparison of gut communities between wild and captive Himalayan griffons. Front Vet Sci 2024; 11:1403932. [PMID: 38784654 PMCID: PMC11112026 DOI: 10.3389/fvets.2024.1403932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Himalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited. Methods In this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions. Results Our results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs). Discussion In summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.
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Affiliation(s)
- You Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Jundie Zhai
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Boyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Yonggang Dong
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Shengzhen Sun
- Animal Disease Prevention and Control Center of Qinghai Province, Xining, Qinghai, China
| | - Shunfu He
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Wenxin Zhao
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Zhuoma Lancuo
- College of Finance and Economics, Qinghai University, Xining, Qinghai, China
| | - Qiangqiang Jia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
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Oliver A, Podell S, Wegley Kelly L, Sparagon WJ, Plominsky AM, Nelson RS, Laurens LML, Augyte S, Sims NA, Nelson CE, Allen EE. Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish. mBio 2024; 15:e0049624. [PMID: 38534158 PMCID: PMC11077953 DOI: 10.1128/mbio.00496-24] [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: 02/21/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce genomic information about the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) from previously described Kyphosus gut metagenomes and newly sequenced bioreactor enrichments reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzyme collections able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea) and Verrucomicrobiota (order Kiritimatiellales) highlight the importance of metabolic contributions from multiple phyla to broaden polysaccharide degradation capabilities. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.IMPORTANCESeaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genus Kyphosus feed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study reconstructs metagenome-assembled genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identify Kyphosus guts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.
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Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Wesley J. Sparagon
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, Honolulu, Hawaii, USA
| | - Alvaro M. Plominsky
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | | | | | | | | | - Craig E. Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, Honolulu, Hawaii, USA
| | - Eric E. Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, USA
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Wang Z, Liu D, Zhang J, Liu L, Zhang Z, Liu C, Hu S, Wu L, He Z, Sun H. Genomic epidemiology reveals multiple mechanisms of linezolid resistance in clinical enterococci in China. Ann Clin Microbiol Antimicrob 2024; 23:41. [PMID: 38704577 PMCID: PMC11070108 DOI: 10.1186/s12941-024-00689-0] [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: 01/24/2024] [Accepted: 03/21/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Infections caused by linezolid-resistant enterococci (LRE) are clinically difficult to treat and threaten patient health. However, there is a lack of studies on long time-span LRE strains in China. For this reason, our study comprehensively revealed the resistance mechanisms of LRE strains collected in a Chinese tertiary care hospital from 2011 to 2022. METHODS Enterococcal strains were screened and verified after retrospective analysis of microbial data. Subsequently, 65 LRE strains (61 Enterococcus faecalis and 4 Enterococcus faecium, MIC ≥ 8 µg/ml), 1 linezolid-intermediate Enterococcus faecium (MIC = 4 µg/ml) and 1 linezolid-susceptible Enterococcus faecium (MIC = 1.5 µg/ml) were submitted for whole-genome sequencing (WGS) analysis and bioinformatics analysis. RESULTS The optrA gene was found to be the most common linezolid resistance mechanism in our study. We identified the wild-type OptrA and various OptrA variants in 98.5% of LRE strains (61 Enterococcus faecalis and 3 Enterococcus faecium). We also found one linezolid-resistant Enterococcus faecium strain carried both optrA and cfr(D) gene, while one linezolid-resistant Enterococcus faecium only harbored the poxtA gene. Most optrA genes (55/64) were located on plasmids, with impB-fexA-optrA, impB-fexA-optrA-erm(A), fexA-optrA-erm(A), and fexA-optrA segments. A minority of optrA genes (9/64) were found on chromosomes with the Tn6674-like platform. Besides, other possible linezolid resistance-associated mechanisms (mutations in the rplC and rplD genes) were also found in 26 enterococcal strains. CONCLUSIONS Our study suggested that multiple mechanisms of linezolid resistance exist among clinical LRE strains in China.
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Affiliation(s)
- Ziran Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing, Dongcheng, Beijing, 100730, P.R. China
| | - Danping Liu
- School of Engineering Medicine, Beihang University, Rd37, xueyuan, Haidian, Beijing, 100191, P.R. China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People's Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| | - Jingjia Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing, Dongcheng, Beijing, 100730, P.R. China
| | - Lingli Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing, Dongcheng, Beijing, 100730, P.R. China
| | - Zeming Zhang
- School of Engineering Medicine, Beihang University, Rd37, xueyuan, Haidian, Beijing, 100191, P.R. China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People's Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| | - Chang Liu
- Department of Clinical Laboratory, Beijing Huaxin Hospital, The First Hospital of Tsinghua University, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Linhuan Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zilong He
- School of Engineering Medicine, Beihang University, Rd37, xueyuan, Haidian, Beijing, 100191, P.R. China.
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People's Republic of China, Beijing, China.
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China.
| | - Hongli Sun
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing, Dongcheng, Beijing, 100730, P.R. China.
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Ke S, Villafuerte Gálvez JA, Sun Z, Cao Y, Pollock NR, Chen X, Kelly CP, Liu YY. Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591969. [PMID: 38746249 PMCID: PMC11092666 DOI: 10.1101/2024.04.30.591969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Clostridioides difficile infection (CDI) is one of the leading causes of healthcare- and antibiotic-associated diarrhea. While fecal microbiota transplantation (FMT) has emerged as a promising therapy for recurrent CDI, its exact mechanisms of action and long-term safety are not fully understood. Defined consortia of clonal bacterial isolates, known as live biotherapeutic products (LBPs), have been proposed as an alternative therapeutic option. However, the rational design of LBPs remains challenging. Here, we employ a computational pipeline and three independent metagenomic datasets to systematically identify microbial strains that have the potential to inhibit CDI. We first constructed the CDI-related microbial genome catalog, comprising 3,741 non-redundant metagenome-assembled genomes (nrMAGs) at the strain level. We then identified multiple potential protective nrMAGs that can be candidates for the design of microbial consortia targeting CDI, including strains from Dorea formicigenerans, Oscillibacter welbionis, and Faecalibacterium prausnitzii. Importantly, some of these potential protective nrMAGs were found to play an important role in the success of FMT, and the majority of the top protective nrMAGs can be validated by various previously reported findings. Our results demonstrate a computational framework for the rational selection of microbial strains targeting CDI, paving the way for the computational design of microbial consortia against other enteric infections.
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Affiliation(s)
- Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Javier A Villafuerte Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Zheng Sun
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yangchun Cao
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Nira R Pollock
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Ciarán P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
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Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S. Generation of accurate, expandable phylogenomic trees with uDance. Nat Biotechnol 2024; 42:768-777. [PMID: 37500914 PMCID: PMC10818028 DOI: 10.1038/s41587-023-01868-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
Phylogenetic trees provide a framework for organizing evolutionary histories across the tree of life and aid downstream comparative analyses such as metagenomic identification. Methods that rely on single-marker genes such as 16S rRNA have produced trees of limited accuracy with hundreds of thousands of organisms, whereas methods that use genome-wide data are not scalable to large numbers of genomes. We introduce updating trees using divide-and-conquer (uDance), a method that enables updatable genome-wide inference using a divide-and-conquer strategy that refines different parts of the tree independently and can build off of existing trees, with high accuracy and scalability. With uDance, we infer a species tree of roughly 200,000 genomes using 387 marker genes, totaling 42.5 billion amino acid residues.
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Affiliation(s)
- Metin Balaban
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Yueyu Jiang
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
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Gou J, Xia J, Li Y, Qiu Y, Jiang F. A novel sulfidogenic process via sulfur reduction to remove arsenate in acid mine drainage: Insights into the performance and microbial mechanisms. WATER RESEARCH 2024; 254:121423. [PMID: 38461598 DOI: 10.1016/j.watres.2024.121423] [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: 01/05/2024] [Revised: 02/24/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Biological sulfidogenic processes based on sulfate-reducing bacteria (SRB) are not suitable for arsenic (As)-containing acid mine drainage (AMD) treatment because of the formation of the mobile thioarsenite during sulfate reduction. In contrast, biological sulfidogenic processes based on sulfur-reducing bacteria (S0RB) produce sulfide without pH increase, which could achieve more effective As removal than the SRB-based process. However, the reduction ability and toxicity tolerance of S0RB to As remains mysterious, which may substantially affect the practical applicability of this process when treating arsenate (As(V))-containing AMD. Thus, this study aims to develop a biological sulfur reduction process driven by S0RB, and explore its long-term performance on As(V) removal and microbial community evolution. Operating under moderately acidic conditions (pH=4.0), the presence of 10 mg/L As(V) significantly suppressed the activity of S0RB, leading to the failure of As(V) removal. Surprisingly, a drop in pH to 3.0 enhanced the tolerance of S0RB to As toxicity, allowing for efficient sulfide production (396±102 mg S/L) through sulfur reduction. Consequently, effective and stable removal of As(V) (99.9 %) was achieved, even though the sulfidogenic bacteria were exposed to high levels of As(V) (42 mg/L) in long-term trials. Spectral and spectroscopic analysis showed that As-bearing sulfide minerals were present in the bioreactor. Remarkably, the presence of As(V) induced notable changes in the microbial community composition, with Desulfurella and Clostridium identified as predominate sulfur reducers. The qPCR result further revealed an increase in the concentration of functional genes related to As transport (asrA and arsB) in the bioreactor sludge as the pH decreased from 4.0 to 3.0. This suggests the involvement of microorganisms carrying asrA and arsB in an As transport process. Furthermore, metagenomic binning demonstrated that Desulfurella contained essential genes associated with sulfur reduction and As transportation, indicating its genetic potential for sulfide production and As tolerance. In summary, this study underscores the effectiveness of the biological sulfur reduction process driven by S0RB in treating As(V)-contaminated AMD. It offers insights into the role of S0RB in remediating As contamination and provides valuable knowledge for practical applications.
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Affiliation(s)
- Jiahua Gou
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Juntao Xia
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu Li
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yanying Qiu
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Feng Jiang
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial International Joint Research Center on Urban Water Management and Treatment, Sun Yat-sen University, Guangzhou 510275, China.
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Quiñonero-Coronel MDM, Devos DP, Garcillán-Barcia MP. Specificities and commonalities of the Planctomycetes plasmidome. Environ Microbiol 2024; 26:e16638. [PMID: 38733104 DOI: 10.1111/1462-2920.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.
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Affiliation(s)
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD, CSIC-Universidad Pablo de Olavide), Sevilla, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, CSIC-Universidad de Cantabria), Cantabria, Spain
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Li J, Chen C, Ji L, Wen S, Peng J, Yang L, He G. Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171364. [PMID: 38438026 DOI: 10.1016/j.scitotenv.2024.171364] [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: 10/03/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024]
Abstract
Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.
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Affiliation(s)
- Jing Li
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Chuxiang Chen
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Li Ji
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China.
| | - Shizhi Wen
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Jun Peng
- Hunan Geological Experiment and Testing Center, Changsha, 290 Middle Chengnan Road, 410007, PR China
| | - Lili Yang
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Gongxiu He
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China.
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49
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Spatola Rossi T, Gallia M, Erijman L, Figuerola E. Biotic and abiotic factors acting on community assembly in parallel anaerobic digestion systems from a brewery wastewater treatment plant. ENVIRONMENTAL TECHNOLOGY 2024:1-16. [PMID: 38686914 DOI: 10.1080/09593330.2024.2343797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
Anaerobic digestion is a complex microbial process that mediates the transformation of organic waste into biogas. The performance and stability of anaerobic digesters relies on the structure and function of the microbial community. In this study, we asked whether the deterministic effect of wastewater composition outweighs the effect of reactor configuration on the structure and dynamics of anaerobic digester archaeal and bacterial communities. Biotic and abiotic factors acting on microbial community assembly in two parallel anaerobic digestion systems, an upflow anaerobic sludge blanket digestor (UASB) and a closed digester tank with a solid recycling system (CDSR), from a brewery WWTP were analysed utilizing 16S rDNA and mcrA amplicon sequencing and genome-centric metagenomics. This study confirmed the deterministic effect of the wastewater composition on bacterial community structure, while the archaeal community composition resulted better explained by organic loading rate (ORL) and volatile free acids (VFA). According to the functions assigned to the differentially abundant metagenome-assembled genomes (MAGs) between reactors, CDSR was enriched in genes related to methanol and methylamines methanogenesis, protein degradation, and sulphate and alcohol utilization. Conversely, the UASB reactor was enriched in genes associated with carbohydrate and lipid degradation, as well as amino acid, fatty acid, and propionate fermentation. By comparing interactions derived from the co-occurrence network with predicted metabolic interactions of the prokaryotic communities in both anaerobic digesters, we conclude that the overall community structure is mainly determined by habitat filtering.
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Affiliation(s)
| | - Mateo Gallia
- IB3- Institute of Biosciences, Biotechnology and Translational Biology- University of Buenos Aires Buenos Aires, Argentina
| | - Leonardo Erijman
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular 'Dr Héctor N. Torres' (INGEBI-CONICET), Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Eva Figuerola
- IB3- Institute of Biosciences, Biotechnology and Translational Biology- University of Buenos Aires Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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50
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Rolando JL, Kolton M, Song T, Liu Y, Pinamang P, Conrad R, Morris JT, Konstantinidis KT, Kostka JE. Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora. Nat Commun 2024; 15:3607. [PMID: 38684658 PMCID: PMC11059160 DOI: 10.1038/s41467-024-47646-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes.
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Affiliation(s)
- J L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - M Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - T Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Y Liu
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- The Pennsylvania State University, Department of Civil & Environmental Engineering, University Park, PA, 16802, USA
| | - P Pinamang
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - R Conrad
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - J T Morris
- Belle Baruch Institute for Marine & Coastal Sciences, University of South Carolina, Columbia, SC, 29201, USA
| | - K T Konstantinidis
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA, 30332, USA
| | - J E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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