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Ryu EP, Gautam Y, Proctor DM, Bhandari D, Tandukar S, Gupta M, Gautam GP, Relman DA, Shibl AA, Sherchand JB, Jha AR, Davenport ER. Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601557. [PMID: 39005279 PMCID: PMC11244963 DOI: 10.1101/2024.07.01.601557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Background Lifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remains less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called 'vanishing microbiomes' potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations. Results Here, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the United States within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain source. Conclusion Our findings demonstrate that by controlling for geography, we can isolate an important role for lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes.
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Affiliation(s)
- Erica P. Ryu
- Department of Biology, Pennsylvania State University, University Park, PA
| | - Yoshina Gautam
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Diana M. Proctor
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Dinesh Bhandari
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
- School of Public Health, University of Adelaide, South Australia, Australia
| | - Sarmila Tandukar
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
- Organization for Public Health and Environment Management, Lalitpur, Bagmati, Nepal
| | - Meera Gupta
- Department of Biology, Pennsylvania State University, University Park, PA
| | | | - David A. Relman
- Departments of Medicine, and of Microbiology & Immunology, Stanford University, Stanford, CA
- Section of Infectious Diseases, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA
| | - Ahmed A. Shibl
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- Center for Genomics and Systems Biology, and Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- Center for Genomics and Systems Biology, and Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Emily R. Davenport
- Department of Biology, Pennsylvania State University, University Park, PA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
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52
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Li DD, Wang J, Jiang Y, Zhang P, Liu Y, Li YZ, Zhang Z. Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities. MICROBIOME 2024; 12:120. [PMID: 38956705 PMCID: PMC11218364 DOI: 10.1186/s40168-024-01838-5] [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: 04/19/2022] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Functional redundancy (FR) is widely present, but there is no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, and distinct assemblies of microorganisms in different communities playing the same functional roles are termed between-community FR. We proposed two formulas to respectively quantify the degree of functional redundancy within and between communities and analyzed the FR degrees of carbohydrate degradation functions in global environment samples using the genetic information of glycoside hydrolases (GHs) encoded by prokaryotes. RESULTS Our results revealed that GHs are each encoded by multiple taxonomically distinct prokaryotes within a community, and the enzyme-encoding prokaryotes are further distinct between almost any community pairs. The within- and between-FR degrees are primarily affected by the alpha and beta community diversities, respectively, and are also affected by environmental factors (e.g., pH, temperature, and salinity). The FR degree of the prokaryotic community is determined by deterministic factors. CONCLUSIONS We conclude that the functional redundancy of GHs is a stabilized community characteristic. This study helps to determine the FR formation process and influencing factors and provides new insights into the relationships between prokaryotic community biodiversity and ecosystem functions. Video Abstract.
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Affiliation(s)
- Dan-Dan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yiru Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Williams SE, Varliero G, Lurgi M, Stach JEM, Race PR, Curnow P. Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39073401 DOI: 10.1099/mic.0.001478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.
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Affiliation(s)
- Sam E Williams
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs., Lyngby, Denmark
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Miguel Lurgi
- Department of Biosciences, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul R Race
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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54
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Yi Y, Liang L, de Jong A, Kuipers OP. A systematic comparison of natural product potential, with an emphasis on RiPPs, by mining of bacteria of three large ecosystems. Genomics 2024; 116:110880. [PMID: 38857812 DOI: 10.1016/j.ygeno.2024.110880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/22/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Abstract
The implementation of several global microbiome studies has yielded extensive insights into the biosynthetic potential of natural microbial communities. However, studies on the distribution of several classes of ribosomally synthesized and post-translationally modified peptides (RiPPs), non-ribosomal peptides (NRPs) and polyketides (PKs) in different large microbial ecosystems have been very limited. Here, we collected a large set of metagenome-assembled bacterial genomes from marine, freshwater and terrestrial ecosystems to investigate the biosynthetic potential of these bacteria. We demonstrate the utility of public dataset collections for revealing the different secondary metabolite biosynthetic potentials among these different living environments. We show that there is a higher occurrence of RiPPs in terrestrial systems, while in marine systems, we found relatively more terpene-, NRP-, and PK encoding gene clusters. Among the many new biosynthetic gene clusters (BGCs) identified, we analyzed various Nif-11-like and nitrile hydratase leader peptide (NHLP) containing gene clusters that would merit further study, including promising products, such as mersacidin-, LAP- and proteusin analogs. This research highlights the significance of public datasets in elucidating the biosynthetic potential of microbes in different living environments and underscores the wide bioengineering opportunities within the RiPP family.
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Affiliation(s)
- Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands
| | | | - Anne de Jong
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands.
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55
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Leapaldt HC, Frantz CM, Olsen-Valdez J, Snell KE, Trower EJ, Ingalls M. Primary to post-depositional microbial controls on the stable and clumped isotope record of shoreline sediments at Fayetteville Green Lake. GEOBIOLOGY 2024; 22:e12609. [PMID: 38958391 DOI: 10.1111/gbi.12609] [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: 06/08/2023] [Revised: 04/22/2024] [Accepted: 06/11/2024] [Indexed: 07/04/2024]
Abstract
Lacustrine carbonates are a powerful archive of paleoenvironmental information but are susceptible to post-depositional alteration. Microbial metabolisms can drive such alteration by changing carbonate saturation in situ, thereby driving dissolution or precipitation. The net impact these microbial processes have on the primary δ18O, δ13C, and Δ47 values of lacustrine carbonate is not fully known. We studied the evolution of microbial community structure and the porewater and sediment geochemistry in the upper ~30 cm of sediment from two shoreline sites at Green Lake, Fayetteville, NY over 2 years of seasonal sampling. We linked seasonal and depth-based changes of porewater carbonate chemistry to microbial community composition, in situ carbon cycling (using δ13C values of carbonate, dissolved inorganic carbon (DIC), and organic matter), and dominant allochems and facies. We interpret that microbial processes are a dominant control on carbon cycling within the sediment, affecting porewater DIC, aqueous carbon chemistry, and carbonate carbon and clumped isotope geochemistry. Across all seasons and sites, microbial organic matter remineralization lowers the δ13C of the porewater DIC. Elevated carbonate saturation states in the sediment porewaters (Ω > 3) were attributed to microbes from groups capable of sulfate reduction, which were abundant in the sediment below 5 cm depth. The nearshore carbonate sediments at Green Lake are mainly composed of microbialite intraclasts/oncoids, charophytes, larger calcite crystals, and authigenic micrite-each with a different origin. Authigenic micrite is interpreted to have precipitated in situ from the supersaturated porewaters from microbial metabolism. The stable carbon isotope values (δ13Ccarb) and clumped isotope values (Δ47) of bulk carbonate sediments from the same depth horizons and site varied depending on both the sampling season and the specific location within a site, indicating localized (μm to mm) controls on carbon and clumped isotope values. Our results suggest that biological processes are a dominant control on carbon chemistry within the sedimentary subsurface of the shorelines of Green Lake, from actively forming microbialites to pore space organic matter remineralization and micrite authigenesis. A combination of biological activity, hydrologic balance, and allochem composition of the sediments set the stable carbon, oxygen, and clumped isotope signals preserved by the Green Lake carbonate sediments.
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Affiliation(s)
- Hanna C Leapaldt
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Carie M Frantz
- Department of Earth and Environmental Sciences, Weber State University, Ogden, Utah, USA
| | - Juliana Olsen-Valdez
- Department of Geological Sciences, University of Colorado, Boulder, Colorado, USA
| | - Kathryn E Snell
- Department of Geological Sciences, University of Colorado, Boulder, Colorado, USA
| | - Elizabeth J Trower
- Department of Geological Sciences, University of Colorado, Boulder, Colorado, USA
| | - Miquela Ingalls
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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56
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Graham EB, Camargo AP, Wu R, Neches RY, Nolan M, Paez-Espino D, Kyrpides NC, Jansson JK, McDermott JE, Hofmockel KS. A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts. Nat Microbiol 2024; 9:1873-1883. [PMID: 38902374 PMCID: PMC11222151 DOI: 10.1038/s41564-024-01686-x] [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: 09/17/2023] [Accepted: 03/25/2024] [Indexed: 06/22/2024]
Abstract
Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.
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Affiliation(s)
- Emily B Graham
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
| | - Antonio Pedro Camargo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Russell Y Neches
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Matt Nolan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Paez-Espino
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Kirsten S Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Agronomy, Iowa State University, Ames, IA, USA
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57
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Chen J, Lin L, Tu Q, Peng Q, Wang X, Liang C, Zhou J, Yu X. Metagenomic-based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database. Mol Ecol Resour 2024; 24:e13950. [PMID: 38567644 DOI: 10.1111/1755-0998.13950] [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: 10/21/2023] [Revised: 02/05/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.
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Affiliation(s)
- Jiyu Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qiannan Peng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaopeng Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Congying Liang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, China
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58
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Huang Z, Cai D, Sun Y. Towards more accurate microbial source tracking via non-negative matrix factorization (NMF). Bioinformatics 2024; 40:i68-i78. [PMID: 38940128 PMCID: PMC11256951 DOI: 10.1093/bioinformatics/btae227] [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] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION The microbiome of a sampled habitat often consists of microbial communities from various sources, including potential contaminants. Microbial source tracking (MST) can be used to discern the contribution of each source to the observed microbiome data, thus enabling the identification and tracking of microbial communities within a sample. Therefore, MST has various applications, from monitoring microbial contamination in clinical labs to tracing the source of pollution in environmental samples. Despite promising results in MST development, there is still room for improvement, particularly for applications where precise quantification of each source's contribution is critical. RESULTS In this study, we introduce a novel tool called SourceID-NMF towards more precise microbial source tracking. SourceID-NMF utilizes a non-negative matrix factorization (NMF) algorithm to trace the microbial sources contributing to a target sample. By leveraging the taxa abundance in both available sources and the target sample, SourceID-NMF estimates the proportion of available sources present in the target sample. To evaluate the performance of SourceID-NMF, we conducted a series of benchmarking experiments using simulated and real data. The simulated experiments mimic realistic yet challenging scenarios for identifying highly similar sources, irrelevant sources, unknown sources, low abundance sources, and noise sources. The results demonstrate the superior accuracy of SourceID-NMF over existing methods. Particularly, SourceID-NMF accurately estimated the proportion of irrelevant and unknown sources while other tools either over- or under-estimated them. In addition, the noise sources experiment also demonstrated the robustness of SourceID-NMF for MST. AVAILABILITY AND IMPLEMENTATION SourceID-NMF is available online at https://github.com/ZiyiHuang0708/SourceID-NMF.
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Affiliation(s)
- Ziyi Huang
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Dehan Cai
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
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59
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Dueholm MKD, Andersen KS, Korntved AKC, Rudkjøbing V, Alves M, Bajón-Fernández Y, Batstone D, Butler C, Cruz MC, Davidsson Å, Erijman L, Holliger C, Koch K, Kreuzinger N, Lee C, Lyberatos G, Mutnuri S, O'Flaherty V, Oleskowicz-Popiel P, Pokorna D, Rajal V, Recktenwald M, Rodríguez J, Saikaly PE, Tooker N, Vierheilig J, De Vrieze J, Wurzbacher C, Nielsen PH. MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters. Nat Commun 2024; 15:5361. [PMID: 38918384 PMCID: PMC11199495 DOI: 10.1038/s41467-024-49641-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.
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Affiliation(s)
- Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Kasper Skytte Andersen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anne-Kirstine C Korntved
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Vibeke Rudkjøbing
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Madalena Alves
- Centre of Biological Engineering, University of Minho, Minho, Portugal
| | | | - Damien Batstone
- Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, Brisbane, Australia
| | - Caitlyn Butler
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Mercedes Cecilia Cruz
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | - Åsa Davidsson
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Leonardo Erijman
- INGEBI-CONICET, University of Buenos Aires, Buenos Aires, Argentina
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Konrad Koch
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Garching, Germany
| | - Norbert Kreuzinger
- Institute of Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Changsoo Lee
- Department of Civil, Urban, Earth, and Environmental Engineering & Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Gerasimos Lyberatos
- School of Chemical Engineering, National Technical University of Athens, Zografou, Greece
| | - Srikanth Mutnuri
- Applied Environmental Biotechnology Laboratory, Birla Institute of Technology and Science (BITS-Pilani), Pilani, Goa campus, Goa, India
| | - Vincent O'Flaherty
- School of Biological and Chemical Sciences and Ryan Institute, University of Galway, Galway, Ireland
| | - Piotr Oleskowicz-Popiel
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Poznan, Poland
| | - Dana Pokorna
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Veronica Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | | | - Jorge Rodríguez
- Chemical Engineering Department, Khalifa University, Khalifa, UAE
| | - Pascal E Saikaly
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Nick Tooker
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Julia Vierheilig
- Institute of Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Garching, Germany
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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Pechlivanis N, Karakatsoulis G, Kyritsis K, Tsagiopoulou M, Sgardelis S, Kappas I, Psomopoulos F. Microbial co-occurrence network demonstrates spatial and climatic trends for global soil diversity. Sci Data 2024; 11:672. [PMID: 38909071 PMCID: PMC11193810 DOI: 10.1038/s41597-024-03528-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024] Open
Abstract
Despite recent research efforts to explore the co-occurrence patterns of diverse microbes within soil microbial communities, a substantial knowledge-gap persists regarding global climate influences on soil microbiota behaviour. Comprehending co-occurrence patterns within distinct geoclimatic groups is pivotal for unravelling the ecological structure of microbial communities, that are crucial for preserving ecosystem functions and services. Our study addresses this gap by examining global climatic patterns of microbial diversity. Using data from the Earth Microbiome Project, we analyse a meta-community co-occurrence network for bacterial communities. This method unveils substantial shifts in topological features, highlighting regional and climatic trends. Arid, Polar, and Tropical zones show lower diversity but maintain denser networks, whereas Temperate and Cold zones display higher diversity alongside more modular networks. Furthermore, it identifies significant co-occurrence patterns across diverse climatic regions. Central taxa associated with different climates are pinpointed, highlighting climate's pivotal role in community structure. In conclusion, our study identifies significant correlations between microbial interactions in diverse climatic regions, contributing valuable insights into the intricate dynamics of soil microbiota.
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Affiliation(s)
- Nikos Pechlivanis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Georgios Karakatsoulis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
| | - Konstantinos Kyritsis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
| | - Maria Tsagiopoulou
- Centro Nacional de Analisis Genomico (CNAG), C/Baldiri Reixac 4, 08028, Barcelona, Spain
| | - Stefanos Sgardelis
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Ilias Kappas
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece.
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61
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Miao J, Chen T, Misir M, Lin Y. Deep learning for predicting 16S rRNA gene copy number. Sci Rep 2024; 14:14282. [PMID: 38902329 PMCID: PMC11190246 DOI: 10.1038/s41598-024-64658-5] [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: 01/24/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Culture-independent 16S rRNA gene metabarcoding is a commonly used method for microbiome profiling. To achieve more quantitative cell fraction estimates, it is important to account for the 16S rRNA gene copy number (hereafter 16S GCN) of different community members. Currently, there are several bioinformatic tools available to estimate the 16S GCN values, either based on taxonomy assignment or phylogeny. Here we present a novel approach ANNA16, Artificial Neural Network Approximator for 16S rRNA gene copy number, a deep learning-based method that estimates the 16S GCN values directly from the 16S gene sequence strings. Based on 27,579 16S rRNA gene sequences and gene copy number data from the rrnDB database, we show that ANNA16 outperforms the commonly used 16S GCN prediction algorithms. Interestingly, Shapley Additive exPlanations (SHAP) shows that ANNA16 can identify unexpected informative positions in 16S rRNA gene sequences without any prior phylogenetic knowledge, which suggests potential applications beyond 16S GCN prediction.
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Affiliation(s)
- Jiazheng Miao
- Division of Applied and Natural Sciences, Duke Kunshan University, Suzhou, China
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Tianlai Chen
- Division of Applied and Natural Sciences, Duke Kunshan University, Suzhou, China
- Department of Biomedical Engineering, Duke University, Durham, USA
| | - Mustafa Misir
- Division of Applied and Natural Sciences, Duke Kunshan University, Suzhou, China.
| | - Yajuan Lin
- Division of Applied and Natural Sciences, Duke Kunshan University, Suzhou, China.
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, USA.
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Bontemps Z, Paranjape K, Guy L. Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts. FEMS Microbiol Rev 2024; 48:fuae021. [PMID: 39081075 PMCID: PMC11338181 DOI: 10.1093/femsre/fuae021] [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: 12/15/2023] [Revised: 07/22/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024] Open
Abstract
Interactions between eukaryotic hosts and their bacterial symbionts drive key ecological and evolutionary processes, from regulating ecosystems to the evolution of complex molecular machines and processes. Over time, endosymbionts generally evolve reduced genomes, and their relationship with their host tends to stabilize. However, host-bacteria relationships may be heavily influenced by environmental changes. Here, we review these effects on one of the most ancient and diverse endosymbiotic groups, formed by-among others-Legionellales, Francisellaceae, and Piscirickettsiaceae. This group is referred to as Deep-branching Intracellular Gammaproteobacteria (DIG), whose last common ancestor presumably emerged about 2 Ga ago. We show that DIGs are globally distributed, but generally at very low abundance, and are mainly identified in aquatic biomes. Most DIGs harbour a type IVB secretion system, critical for host-adaptation, but its structure and composition vary. Finally, we review the different types of microbial interactions that can occur in diverse environments, with direct or indirect effects on DIG populations. The increased use of omics technologies on environmental samples will allow a better understanding of host-bacterial interactions and help unravel the definition of DIGs as a group from an ecological, molecular, and evolutionary perspective.
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Affiliation(s)
- Zélia Bontemps
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75237 Uppsala, Sweden
| | - Kiran Paranjape
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75237 Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75237 Uppsala, Sweden
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63
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Yu L, Li D, Zhang Y, Wang Y, Yao Q, Yang K. An optimal combined slow-release nitrogen fertilizer and urea can enhance the decomposition rate of straw and the yield of maize by improving soil bacterial community and structure under full straw returning system. Front Microbiol 2024; 15:1358582. [PMID: 38962118 PMCID: PMC11219627 DOI: 10.3389/fmicb.2024.1358582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/06/2024] [Indexed: 07/05/2024] Open
Abstract
Under a full straw returning system, the relationship between soil bacterial community diversity and straw decomposition, yield, and the combined application of slow-release nitrogen and urea remains unclear. To evaluate these effects and provide an effective strategy for sustainable agricultural production, a 2-year field positioning trial was conducted using maize as the research object. Six experimental treatments were set up: straw returning + no nitrogen fertilizer (S1N0), straw returning + slow-release nitrogen fertilizer:urea = 0:100% (S1N1), straw returning + slow-release nitrogen fertilizer:urea = 30%:70% (S1N2), straw returning + slow-release nitrogen fertilizer:urea = 60%:40% (S1N3), straw returning + slow-release nitrogen fertilizer:urea = 90%:10% (S1N4), and straw removal + slow-release nitrogen fertilizer:urea = 30%:70% (S0N2). Significant differences (p < 0.05) were observed between treatments for Proteobacteria, Acidobacteriota, Myxococcota, and Actinobacteriota at the jointing stage; Proteobacteria, Acidobacteriota, Myxococcota, Bacteroidota, and Gemmatimonadota at the tasseling stage; and Bacteroidota, Firmicutes, Myxococcota, Methylomirabilota, and Proteobacteria at the maturity stage. The alpha diversity analysis of the soil bacterial community showed that the number of operational taxonomic units (OTUs) and the Chao1 index were higher in S1N2, S1N3, and S1N4 compared with S0N2 at each growth stage. Additionally, the alpha diversity measures were higher in S1N3 and S1N4 compared with S1N2. The beta diversity analysis of the soil bacterial community showed that the bacterial communities in S1N3 and S1N4 were more similar or closely clustered together, while S0N2 was further from all treatments across the three growth stages. The cumulative straw decomposition rate was tested for each treatment, and data showed that S1N3 (90.58%) had the highest decomposition rate. At the phylum level, straw decomposition was positively correlated with Proteobacteria, Actinobacteriota, Myxococcota, and Bacteroidota but significantly negatively correlated with Acidobacteriota. PICRUSt2 function prediction results show that the relative abundance of bacteria in soil samples from each treatment differed significantly. The maize yield of S1N3 was 15597.85 ± 1477.17 kg/hm2, which was 12.80 and 4.18% higher than that of S1N1 and S0N2, respectively. In conclusion, a combination of slow-release nitrogen fertilizer and urea can enhance the straw decomposition rate and maize yield by improving the soil bacterial community and structure within a full straw returning system.
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Affiliation(s)
- Lihong Yu
- Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Duo Li
- Daqing Agricultural Technology Extension Center, Daqing, China
| | - Yifei Zhang
- Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yufeng Wang
- Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Qin Yao
- Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Kejun Yang
- Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
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64
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Graham EB, Garayburu-Caruso VA, Wu R, Zheng J, McClure R, Jones GD. Genomic fingerprints of the world's soil ecosystems. mSystems 2024; 9:e0111223. [PMID: 38722174 PMCID: PMC11237643 DOI: 10.1128/msystems.01112-23] [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: 10/18/2023] [Accepted: 03/25/2024] [Indexed: 06/19/2024] Open
Abstract
Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.
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Affiliation(s)
- Emily B. Graham
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | | | - Ruonan Wu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jianqiu Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ryan McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gerrad D. Jones
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, Oregon, USA
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65
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Rodriguez CI, Isobe K, Martiny JBH. Short-term dietary fiber interventions produce consistent gut microbiome responses across studies. mSystems 2024; 9:e0013324. [PMID: 38742890 PMCID: PMC11237734 DOI: 10.1128/msystems.00133-24] [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: 01/29/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify generally (on average) consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2,564 fecal samples from 538 subjects across all interventions. Short-term increases in dietary fiber consumption resulted in highly consistent gut bacterial community responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (vs 82% of variation attributed to the individual), reduced alpha-diversity, and resulted in phylogenetically conserved responses in relative abundances among bacterial taxa. Additionally, we identified bacterial clades, at approximately the genus level, that were highly consistent in their response (on average, increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies. IMPORTANCE Our study is an example of the power of synthesizing and reanalyzing 16S rRNA microbiome data from many intervention studies. Despite high inter-individual variation of the composition of the human gut microbiome, dietary fiber interventions cause a consistent response both in the degree of change and the particular taxa that respond to increased fiber.
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Affiliation(s)
- Cynthia I. Rodriguez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Kazuo Isobe
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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66
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Li C, Liu C, Li H, Liao H, Xu L, Yao M, Li X. The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps. FEMS Microbiol Ecol 2024; 100:fiae087. [PMID: 38866720 PMCID: PMC11212663 DOI: 10.1093/femsec/fiae087] [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: 01/15/2024] [Revised: 04/26/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024] Open
Abstract
Many R packages provide statistical approaches for elucidating the diversity of soil microbes, yet they still struggle to visualize microbial traits on a geographical map. This creates challenges in interpreting microbial biogeography on a regional scale, especially when the spatial scale is large or the distribution of sampling sites is uneven. Here, we developed a lightweight, flexible, and user-friendly R package called microgeo. This package integrates many functions involved in reading, manipulating, and visualizing geographical boundary data; downloading spatial datasets; and calculating microbial traits and rendering them onto a geographical map using grid-based visualization, spatial interpolation, or machine learning. Using this R package, users can visualize any trait calculated by microgeo or other tools on a map and can analyze microbiome data in conjunction with metadata derived from a geographical map. In contrast to other R packages that statistically analyze microbiome data, microgeo provides more-intuitive approaches in illustrating the biogeography of soil microbes on a large geographical scale, serving as an important supplement to statistically driven comparisons and facilitating the biogeographic analysis of publicly accessible microbiome data at a large spatial scale in a more convenient and efficient manner. The microgeo R package can be installed from the Gitee (https://gitee.com/bioape/microgeo) and GitHub (https://github.com/ChaonanLi/microgeo) repositories. Detailed tutorials for the microgeo R package are available at https://chaonanli.github.io/microgeo.
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Affiliation(s)
- Chaonan Li
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
| | - Chi Liu
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hankang Li
- Department of Electrical Engineering and Computer Science, University of California, Irvine, CA 92697, United States
| | - Haijun Liao
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Normal University of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
| | - Lin Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Minjie Yao
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiangzhen Li
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Chen S, Yu G, Long F, Zheng J, Wang Z, Ji X, Guo Q, Wang Z. Growth Stage-Dependent Variation in Soil Quality and Microbial Diversity of Ancient Gleditsia sinensis. Mol Biotechnol 2024:10.1007/s12033-024-01097-7. [PMID: 38833086 DOI: 10.1007/s12033-024-01097-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/21/2024] [Indexed: 06/06/2024]
Abstract
The environment monitoring of forest is vital for the ecosystem sustainable management, especially soil quality. Ancient Gleditsia sinensis is one of the most distributed ancient trees in Shaanxi. Comprehensive soil evaluate is important for the ancient tree protection. In this study, we selected the most distributed ancient tree Gleditsia sinensis and immature tree to compare the effect of growth stage to soil quality and soil bacteria. Most ancient tree soil nutrients were in good condition compared with immature tree. The bacterial community were composed with Proteobacteria (27.55%), Acidobacteriota (16.82%), Actinobacteriota (15.77%), Gemmatimonadota (6.82%), Crenarchaeota (4.61%), Bacteroidota (4.41%), Firmicutes (4.32%), Chloroflexi (4.28%), Planctomycetota (3.24%) and Verrucomicrobiota (3.04%). The level 2 ancient tree (300-400 years old) was different in bacterial community diversity. SOC and STN were important to level 2 (300-400 years old Gleditsia sinensis), and other levels were opposite. Our results suggested that the ancient tree management should not be lumped together.
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Affiliation(s)
- Sihui Chen
- Department of Ecological Environmental Engineering, Yangling Vocational and Technical College, Yangling, 712100, Shaanxi, People's Republic of China
| | - Ge Yu
- Department of Ecological Environmental Engineering, Yangling Vocational and Technical College, Yangling, 712100, Shaanxi, People's Republic of China
| | - Fenglai Long
- Department of Chemistry and Pharmacy, Yangling Vocational and Technical College, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jian Zheng
- Xi'an HuYi District Forest Resources Management Center, Xi'an, 710300, Shaanxi, People's Republic of China
| | - Zeyuan Wang
- Department of Ecological Environmental Engineering, Yangling Vocational and Technical College, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xiaolian Ji
- Department of Ecological Environmental Engineering, Yangling Vocational and Technical College, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qiuping Guo
- Zhouzhi County Agricultural Product Quality Safety Inspection and Monitoring Center, Xi'an, 710400, Shaanxi, People's Republic of China
| | - Zhousuo Wang
- Department of Ecological Environmental Engineering, Yangling Vocational and Technical College, Yangling, 712100, Shaanxi, People's Republic of China.
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68
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Benton LD, Lopez-Galvez N, Herman C, Caporaso JG, Cope EK, Rosales C, Gameros M, Lothrop N, Martínez FD, Wright AL, Carr TF, Beamer PI. Environmental and structural factors associated with bacterial diversity in household dust across the Arizona-Sonora border. Sci Rep 2024; 14:12803. [PMID: 38834753 PMCID: PMC11150412 DOI: 10.1038/s41598-024-63356-6] [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: 09/04/2023] [Accepted: 05/28/2024] [Indexed: 06/06/2024] Open
Abstract
We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs. 8.4%). This investigation assessed differences in microbial dust composition in relation to demographic and housing characteristics on both sides of the US-MX Border. Forty homes were recruited in the US and MX. Home visits collected floor dust and documented occupants' demographics, asthma prevalence, housing structure, and use characteristics. US households were more likely to have inhabitants who reported asthma when compared with MX households (30% vs. 5%) and had significantly different flooring types. The percentage of households on paved roads, with flushing toilets, with piped water and with air conditioning was higher in the US, while dust load was higher in MX. Significant differences exist between countries in the microbial composition of the floor dust. Dust from Mexican homes was enriched with Alishewanella, Paracoccus, Rheinheimera genera and Intrasporangiaceae family. A predictive metagenomics analysis identified 68 significantly differentially abundant functional pathways between US and MX. This study documented multiple structural, environmental, and demographic differences between homes in the US and MX that may contribute to significantly different microbial composition of dust observed in these two countries.
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Affiliation(s)
- Lauren D Benton
- Department of Pediatrics, Steele Children's Research Center, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA.
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA.
| | - Nicolas Lopez-Galvez
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
- San Diego State University Research Foundation, San Diego State University, 5250 Campanile Dr, San Diego, CA, 92182, USA
| | - Chloe Herman
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, 1350 S Knoles Dr, Flagstaff, AZ, 86011, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, 1350 S Knoles Dr, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily K Cope
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, 1350 S Knoles Dr, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Cecilia Rosales
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
| | - Mercedes Gameros
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
| | - Nathan Lothrop
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
| | - Fernando D Martínez
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
| | - Anne L Wright
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
| | - Tara F Carr
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
| | - Paloma I Beamer
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
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69
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Kifushi M, Nishikawa Y, Hosokawa M, Ide K, Kogawa M, Anai T, Takeyama H. Analysis of microbial dynamics in the soybean root-associated environments from community to single-cell levels. J Biosci Bioeng 2024; 137:429-436. [PMID: 38570219 DOI: 10.1016/j.jbiosc.2024.02.007] [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: 09/22/2023] [Revised: 01/04/2024] [Accepted: 02/20/2024] [Indexed: 04/05/2024]
Abstract
Plant root-associated environments such as the rhizosphere, rhizoplane, and endosphere, are notably different from non-root-associated soil environments. However, the microbial dynamics in these spatially divided compartments remain unexplored. In this study, we propose a combinational analysis of single-cell genomics with 16S rRNA gene sequencing. This method enabled us to understand the entire soil microbiome and individual root-associated microorganisms. We applied this method to soybean microbiomes and revealed that their composition was different between the rhizoplane and rhizosphere in the early growth stages, but became more similar as growth progressed. In addition, a total of 610 medium- to high-quality single-amplified genomes (SAGs) were acquired, including plant growth-promoting rhizobacteria (PGPR) candidates while genomes with high GC content tended to be missed by SAGs. The whole-genome analyses of the SAGs suggested that rhizoplane-enriched Flavobacterium solubilizes organophosphate actively and Bacillus colonizes roots more efficiently. Single-cell genomics, together with 16S rRNA gene sequencing, enabled us to connect microbial taxonomy and function, and assess microorganisms at a strain resolution even in the complex soil microbiome.
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Affiliation(s)
- Masako Kifushi
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yohei Nishikawa
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Masahito Hosokawa
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Keigo Ide
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Masato Kogawa
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Haruko Takeyama
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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Zarantonello G, Cuenca A. Nanopore-Enabled Microbiome Analysis: Investigating Environmental and Host-Associated Samples in Rainbow Trout Aquaculture. Curr Protoc 2024; 4:e1069. [PMID: 38865207 DOI: 10.1002/cpz1.1069] [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]
Abstract
Microbiome sequencing is at the forefront of health management development, and as such, it is becoming of great interest to monitor the microbiome in the aquaculture industry as well. Oxford Nanopore Technologies (ONT) platforms are gaining popularity to study microbial communities, enabling faster sequencing, extended read length, and therefore, improved taxonomic resolution. Despite this, there is a lack of clear guidelines to perform a metabarcoding study, especially when dealing with samples from non-mammalian species, such as aquaculture-related samples. In this article, we provide general guidelines for sampling, nucleic acid extraction, and ONT-based library preparation for both environmental (water, sediment) and host-associated (gill or skin mucus, skin, gut content, or gut mucosa) microbiome analysis. Our procedures focus specifically on rainbow trout (Oncorhynchus mykiss) reared in experimental facilities. However, these protocols can also be transferred to alternative types of samples, such as environmental DNA (eDNA) monitoring from alternative water sources, or to different fish species. The additional challenge posed by the low biomass and limited bacterial diversity inherent in fish-associated microbiomes is addressed through the implementation of troubleshooting solutions. Furthermore, we describe a bioinformatic pipeline starting from raw reads and leading to taxonomic abundance tables using currently available tools and software. Finally, we provide a set of specific guidelines and considerations related to the strategic planning of a microbiome study within the context of aquaculture. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Environmental sample collection Basic Protocol 2: Host-associated sample collection Alternate Protocol: Host-associated sample collection: Alternative sample types Basic Protocol 3: Sample pre-treatment and nucleic acid extraction Basic Protocol 4: Quality control and preparation for 16S rRNA gene sequencing Support Protocol 1: Assessment of inhibition by quantitative PCR Support Protocol 2: Bioinformatic analysis from raw files to taxonomic abundance tables.
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Affiliation(s)
- Giulia Zarantonello
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Argelia Cuenca
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
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71
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Tsang CTT, Hui TKL, Chung NM, Yuen WT, Tsang LM. Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification. Mol Ecol 2024; 33:e17377. [PMID: 38713089 DOI: 10.1111/mec.17377] [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: 09/13/2023] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/08/2024]
Abstract
The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont.
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Affiliation(s)
- Chandlar Tsz To Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tom Kwok Lun Hui
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nga Man Chung
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing Tan Yuen
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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72
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Walsh CJ, Srinivas M, Stinear TP, van Sinderen D, Cotter PD, Kenny JG. GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences. Microb Genom 2024; 10:001255. [PMID: 38847800 PMCID: PMC11261877 DOI: 10.1099/mgen.0.001255] [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: 02/02/2024] [Accepted: 05/07/2024] [Indexed: 07/24/2024] Open
Abstract
Sequence comparison of 16S rRNA PCR amplicons is an established approach to taxonomically identify bacterial isolates and profile complex microbial communities. One potential application of recent advances in long-read sequencing technologies is to sequence entire rRNA operons and capture significantly more phylogenetic information compared to sequencing of the 16S rRNA (or regions thereof) alone, with the potential to increase the proportion of amplicons that can be reliably classified to lower taxonomic ranks. Here we describe GROND (Genome-derived Ribosomal Operon Database), a publicly available database of quality-checked 16S-ITS-23S rRNA operons, accompanied by multiple taxonomic classifications. GROND will aid researchers in analysis of their data and act as a standardised database to allow comparison of results between studies.
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Affiliation(s)
- Calum J. Walsh
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, 792 Elizabeth Street, Melbourne VIC 3000, Australia
| | - Meghana Srinivas
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Timothy P. Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, 792 Elizabeth Street, Melbourne VIC 3000, Australia
| | - Douwe van Sinderen
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc Moorepark, Cork, Ireland
| | - John G. Kenny
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc Moorepark, Cork, Ireland
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Rolon ML, Voloshchuk O, Bartlett KV, LaBorde LF, Kovac J. Multi-species biofilms of environmental microbiota isolated from fruit packing facilities promoted tolerance of Listeria monocytogenes to benzalkonium chloride. Biofilm 2024; 7:100177. [PMID: 38304489 PMCID: PMC10832383 DOI: 10.1016/j.bioflm.2024.100177] [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: 11/07/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Listeria monocytogenes may survive and persist in food processing environments due to formation of complex multi-species biofilms of environmental microbiota that co-exists in these environments. This study aimed to determine the effect of selected environmental microbiota on biofilm formation and tolerance of L. monocytogenes to benzalkonium chloride in formed biofilms. The studied microbiota included bacterial families previously shown to co-occur with L. monocytogenes in tree fruit packing facilities, including Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae. Biofilm formation ability and the effect of formed biofilms on the tolerance of L. monocytogenes to benzalkonium chloride was measured in single- and multi-family assemblages. Biofilms were grown statically on polystyrene pegs submerged in a R2A broth. Biofilm formation was quantified using a crystal violet assay, spread-plating, confocal laser scanning microscopy, and its composition was assessed using amplicon sequencing. The concentration of L. monocytogenes in biofilms was determined using the most probable number method. Biofilms were exposed to the sanitizer benzalkonium chloride, and the death kinetics of L. monocytogenes were quantified using a most probable number method. A total of 8, 8, 6, and 3 strains of Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae, respectively, were isolated from the environmental microbiota of tree fruit packing facilities and were used in this study. Biofilms formed by Pseudomonadaceae, Xanthomonadaceae, and all multi-family assemblages had significantly higher concentration of bacteria, as well as L. monocytogenes, compared to biofilms formed by L. monocytogenes alone. Furthermore, multi-family assemblage biofilms increased the tolerance of L. monocytogenes to benzalkonium chloride compared to L. monocytogenes mono-species biofilms and planktonic multi-family assemblages. These findings suggest that L. monocytogenes control strategies should focus not only on assessing the efficacy of sanitizers against L. monocytogenes, but also against biofilm-forming microorganisms that reside in the food processing built environment, such as Pseudomonadaceae or Xanthomonadaceae.
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Affiliation(s)
- M. Laura Rolon
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Olena Voloshchuk
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Katelyn V. Bartlett
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Luke F. LaBorde
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
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Ahmed O, Boucher C, Langmead B. Cliffy: robust 16S rRNA classification based on a compressed LCA index. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595899. [PMID: 38854039 PMCID: PMC11160684 DOI: 10.1101/2024.05.25.595899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Taxonomic sequence classification is a computational problem central to the study of metagenomics and evolution. Advances in compressed indexing with the r -index enable full-text pattern matching against large sequence collections. But the data structures that link pattern sequences to their clades of origin still do not scale well to large collections. Previous work proposed the document array profiles, which use 𝒪 ( rd ) words of space where r is the number of maximal-equal letter runs in the Burrows-Wheeler transform and d is the number of distinct genomes. The linear dependence on d is limiting, since real taxonomies can easily contain 10,000s of leaves or more. We propose a method called cliff compression that reduces this size by a large factor, over 250x when indexing the SILVA 16S rRNA gene database. This method uses Θ( r log d ) words of space in expectation under a random model we propose here. We implemented these ideas in an open source tool called Cliffy that performs efficient taxonomic classification of sequencing reads with respect to a compressed taxonomic index. When applied to simulated 16S rRNA reads, Cliffy's read-level accuracy is higher than Kraken2's by 11-18%. Clade abundances are also more accurately predicted by Cliffy compared to Kraken2 and Bracken. Overall, Cliffy is a fast and space-economical extension to compressed full-text indexes, enabling them to perform fast and accurate taxonomic classification queries. 2012 ACM Subject Classification Applied computing → Computational genomics.
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75
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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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Palacios N, Gordon S, Wang T, Burk R, Qi Q, Huttenhower C, Gonzalez HM, Knight R, De Carli C, Daviglus M, Lamar M, Telavera G, Tarraf W, Kosciolek T, Cai J, Kaplan RC. Gut Microbiome Multi-Omics and Cognitive Function in the Hispanic Community Health Study/Study of Latinos- Investigation of Neurocognitive Aging. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.17.24307533. [PMID: 38798527 PMCID: PMC11118626 DOI: 10.1101/2024.05.17.24307533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
INTRODUCTION We conducted a study within the Hispanic Community Health Study/Study of Latinos- Investigation of Neurocognitive Aging (HCHS/SOL-INCA) cohort to examine the association between gut microbiome and cognitive function. METHODS We analyzed the fecal metagenomes of 2,471 HCHS/SOL-INCA participants to, cross-sectionally, identify microbial taxonomic and functional features associated with global cognitive function. Omnibus (PERMANOVA) and feature-wise analyses (MaAsLin2) were conducted to identify microbiome-cognition associations, and specific microbial species and pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG modules) associated with cognition. RESULTS Eubacterium species( E. siraeum and E. eligens ), were associated with better cognition. Several KEGG modules, most strongly Ornithine, Serine biosynthesis and Urea Cycle, were associated with worse cognition. DISCUSSION In a large Hispanic/Latino cohort, we identified several microbial taxa and KEGG pathways associated with cognition.
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77
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Xiao W, Weissman JL, Johnson PLF. Ecological drivers of CRISPR immune systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594560. [PMID: 38952799 PMCID: PMC11216370 DOI: 10.1101/2024.05.16.594560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
CRISPR-Cas is the only known adaptive immune system of prokaryotes. It is a powerful defense system against mobile genetic elements such as bacteriophages. While CRISPR-Cas systems can be found throughout the prokaryotic tree of life, they are distributed unevenly across taxa and environments. Since adaptive immunity is more useful in environments where pathogens persist or reoccur, the density and/or diversity of the host/pathogen community may drive the uneven distribution of CRISPR system. We directly tested hypotheses connecting CRISPR incidence with prokaryotic density/diversity by analyzing 16S rRNA and metagenomic data from publicly available environmental sequencing projects. In terms of density, we found that CRISPR systems are significantly favored in lower abundance (less dense) taxa and disfavored in higher abundance taxa, at least in marine environments. When we extended this work to compare taxonomic diversity between samples, we found CRISPR system incidence strongly correlated with diversity in human oral environments. Together, these observations confirm that, at least in certain types of environments, the prokaryotic ecological context indeed plays a key role in selecting for CRISPR immunity. Importance 2Microbes must constantly defend themselves against viral pathogens, and a large proportion of prokaryotes do so using the highly effective CRISPR-Cas adaptive immune system. However, many prokaryotes do not. We investigated the ecological factors behind this uneven distribution of CRISPR-Cas immune systems in natural microbial populations. We found strong patterns linking CRISPR-Cas systems to prokaryotic density within ocean environments and to prokaryotic diversity within human oral environments. Our study validates previous within-lab experimental results that suggested these factors might be important and confirms that local environment and ecological context interact to select for CRISPR immunity.
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Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [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: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
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Jurburg SD, Blowes SA, Shade A, Eisenhauer N, Chase JM. Synthesis of recovery patterns in microbial communities across environments. MICROBIOME 2024; 12:79. [PMID: 38711157 DOI: 10.1186/s40168-024-01802-3] [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: 12/08/2023] [Accepted: 03/25/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns. RESULTS To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle. CONCLUSIONS This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract.
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Affiliation(s)
- Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany.
- Institute of Biology, Leipzig University, 04103, Leipzig, Germany.
| | - Shane A Blowes
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, 06108, Halle (Saale), Halle, Germany
| | - Ashley Shade
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Universite Claude Bernard Lyon 1, 69622, Villeurbanne, France
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, 04103, Leipzig, Germany
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, 06108, Halle (Saale), Halle, Germany
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Sampaio Dotto Fiuza B, Machado de Andrade C, Meirelles PM, Santos da Silva J, de Jesus Silva M, Vila Nova Santana C, Pimentel Pinheiro G, Mpairwe H, Cooper P, Brooks C, Pembrey L, Taylor S, Douwes J, Cruz ÁA, Barreto ML, Pearce N, Figueiredo CA. Gut microbiome signature and nasal lavage inflammatory markers in young people with asthma. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100242. [PMID: 38585449 PMCID: PMC10998106 DOI: 10.1016/j.jacig.2024.100242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/04/2023] [Accepted: 12/24/2023] [Indexed: 04/09/2024]
Abstract
Background Asthma is a complex disease and a severe global public health problem resulting from interactions between genetic background and environmental exposures. It has been suggested that gut microbiota may be related to asthma development; however, such relationships needs further investigation. Objective This study aimed to characterize the gut microbiota as well as the nasal lavage cytokine profile of asthmatic and nonasthmatic individuals. Methods Stool and nasal lavage samples were collected from 29 children and adolescents with type 2 asthma and 28 children without asthma in Brazil. Amplicon sequencing of the stool bacterial V4 region of the 16S rRNA gene was performed using Illumina MiSeq. Microbiota analysis was performed by QIIME 2 and PICRUSt2. Type 2 asthma phenotype was characterized by high sputum eosinophil counts and positive skin prick tests for house dust mite, cockroach, and/or cat or dog dander. The nasal immune marker profile was assessed using a customized multiplex panel. Results Stool microbiota differed significantly between asthmatic and nonasthmatic participants (P = .001). Bacteroides was more abundant in participants with asthma (P < .05), while Prevotella was more abundant in nonasthmatic individuals (P < .05). In people with asthma, the relative abundance of Bacteroides correlated with IL-4 concentration in nasal lavage samples. Inference of microbiota functional capacity identified differential fatty acid biosynthesis in asthmatic compared to nonasthmatic subjects. Conclusion The stool microbiota differed between asthmatic and nonasthmatic young people in Brazil. Asthma was associated with higher Bacteroides levels, which correlated with nasal IL-4 concentration.
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Affiliation(s)
| | | | - Pedro Milet Meirelles
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia em Estudos Interdisciplinares e Transdisciplinares em Ecologia e Evolução (IN-TREE), Salvador, Brazil
| | | | | | | | | | | | - Philip Cooper
- Fundacion Ecuatoriana Para Investigacion en Salud, Quito, Ecuador
- Universidad Internacional del Ecuador, Quito, Ecuador
- St George’s University of London, London, United Kingdom
| | - Collin Brooks
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Lucy Pembrey
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Steven Taylor
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Jeroen Douwes
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Álvaro A. Cruz
- Fundação ProAR Salvador, Salvador, Brazil
- Faculdade de Medicina, Universidade Federal da Bahia, Salvador, Brazil
| | - Mauricio L. Barreto
- Centro de Integração de Dados e Conhecimentos para Saúde, Fiocruz, Salvador, Brazil
| | - Neil Pearce
- Centre for Public Health Research, Massey University, Wellington, New Zealand
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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81
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Hossain AA, Pigli YZ, Baca CF, Heissel S, Thomas A, Libis VK, Burian J, Chappie JS, Brady SF, Rice PA, Marraffini LA. DNA glycosylases provide antiviral defence in prokaryotes. Nature 2024; 629:410-416. [PMID: 38632404 PMCID: PMC11078745 DOI: 10.1038/s41586-024-07329-9] [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: 05/19/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Bacteria have adapted to phage predation by evolving a vast assortment of defence systems1. Although anti-phage immunity genes can be identified using bioinformatic tools, the discovery of novel systems is restricted to the available prokaryotic sequence data2. Here, to overcome this limitation, we infected Escherichia coli carrying a soil metagenomic DNA library3 with the lytic coliphage T4 to isolate clones carrying protective genes. Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria. Our study highlights the benefits of screening unsequenced DNA and reveals prokaryotic DNA glycosylases as important players in the bacteria-phage arms race.
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Affiliation(s)
- Amer A Hossain
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Ying Z Pigli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Christian F Baca
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alexis Thomas
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Vincent K Libis
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Ján Burian
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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82
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Lofgren L, Nguyen NH, Kennedy P, Pérez-Pazos E, Fletcher J, Liao HL, Wang H, Zhang K, Ruytinx J, Smith AH, Ke YH, Cotter HVT, Engwall E, Hameed KM, Vilgalys R, Branco S. Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. THE NEW PHYTOLOGIST 2024; 242:1448-1475. [PMID: 38581203 PMCID: PMC11045321 DOI: 10.1111/nph.19700] [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: 07/28/2023] [Accepted: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.
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Affiliation(s)
- Lotus Lofgren
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawai‘i at Māno, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Eduardo Pérez-Pazos
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Jessica Fletcher
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Haihua Wang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
| | - Joske Ruytinx
- Research Group of Microbiology and Plant Genetics, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium, USA
| | - Alexander H. Smith
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Yi-Hong Ke
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109, USA
| | - H. Van T. Cotter
- University of North Carolina at Chapel Hill Herbarium, 120 South Road, Chapel Hill, NC 27599, USA
| | - Eiona Engwall
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599, USA
| | - Khalid M. Hameed
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
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83
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McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol 2024; 42:715-718. [PMID: 37500913 PMCID: PMC10818020 DOI: 10.1038/s41587-023-01845-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/25/2023] [Indexed: 07/29/2023]
Abstract
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
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Affiliation(s)
- Daniel McDonald
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Yueyu Jiang
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Metin Balaban
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - James T Morton
- Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Giorgia Nicolaou
- Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Søren M Karst
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Todd DeSantis
- Department of Informatics, Second Genome, Brisbane, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Andrew Bartko
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Aki S Havulinna
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland
| | | | - Susan Cheng
- Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Mohit Jain
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Computer Science and 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.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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Jurburg SD, Álvarez Blanco MJ, Chatzinotas A, Kazem A, König-Ries B, Babin D, Smalla K, Cerecetto V, Fernandez-Gnecco G, Covacevich F, Viruel E, Bernaschina Y, Leoni C, Garaycochea S, Terra JA, Fresia P, Figuerola ELM, Wall LG, Covelli JM, Agnello AC, Nieto EE, Festa S, Dominici LE, Allegrini M, Zabaloy MC, Morales ME, Erijman L, Coniglio A, Cassán FD, Nievas S, Roldán DM, Menes R, Jauri PV, Marrero CS, Massa AM, Revetria MAM, Fernández-Scavino A, Pereira-Mora L, Martínez S, Frene JP. Datathons: fostering equitability in data reuse in ecology. Trends Microbiol 2024; 32:415-418. [PMID: 38519354 DOI: 10.1016/j.tim.2024.02.010] [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: 11/17/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Approaches to rapidly collecting global biodiversity data are increasingly important, but biodiversity blind spots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to date and formed collaborative consortia for microbiome data synthesis.
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Affiliation(s)
- Stephanie D Jurburg
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany.
| | - María J Álvarez Blanco
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany.
| | - Antonis Chatzinotas
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Anahita Kazem
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany; Department of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Thüringen, Germany
| | - Birgitta König-Ries
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany; Department of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Thüringen, Germany
| | - Doreen Babin
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Victoria Cerecetto
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany; Instituto Nacional de Investigación Agropecuaria (INIA), Área de Recursos Naturales, Producción y Ambiente, Estación Experimental INIA Las Brujas, Ruta 48 km 10, Canelones, Uruguay
| | - Gabriela Fernandez-Gnecco
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany; Instituto de Investigaciones en Biodiversidad y Biotecnología-Consejo Nacional de Investigaciones Científicas y Técnicas (INBIOTEC-CONICET), Mar del Plata, Buenos Aires, Argentina
| | - Fernanda Covacevich
- Instituto de Investigaciones en Biodiversidad y Biotecnología-Consejo Nacional de Investigaciones Científicas y Técnicas (INBIOTEC-CONICET), Mar del Plata, Buenos Aires, Argentina; Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce (INTA, EEA Balcarce), Balcarce, Buenos Aires, Argentina
| | - Emilce Viruel
- Instituto de Investigación Animal del Chaco Semiárido (IIACS), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Tucumán, Argentina
| | - Yesica Bernaschina
- Instituto Nacional de Investigación Agropecuaria (INIA), Sistema Vegetal Intensivo, Estación Experimental INIA Las Brujas, Ruta 48 km 10, Canelones, Uruguay
| | - Carolina Leoni
- Instituto Nacional de Investigación Agropecuaria (INIA), Área de Recursos Naturales, Producción y Ambiente, Estación Experimental INIA Las Brujas, Ruta 48 km 10, Canelones, Uruguay; Instituto Nacional de Investigación Agropecuaria (INIA), Sistema Vegetal Intensivo, Estación Experimental INIA Las Brujas, Ruta 48 km 10, Canelones, Uruguay
| | - Silvia Garaycochea
- Instituto Nacional de Investigación Agropecuaria (INIA), Área de Recursos Naturales, Producción y Ambiente, Estación Experimental INIA Las Brujas, Ruta 48 km 10, Canelones, Uruguay; Instituto Nacional de Investigación Agropecuaria (INIA), Área Mejoramiento Genético y Biotecnología Vegetal, Estación Experimental INIA Las Brujas, Ruta 48 km 10, Canelones, Uruguay
| | - Jose A Terra
- Instituto Nacional de Investigación Agropecuaria (INIA), Sistema Arroz-Ganadería, Estación Experimental INIA Treinta y Tres, Ruta 8 km 282, Treinta y Tres, Uruguay
| | - Pablo Fresia
- Unidad Mixta Pasteur + INIA (UMPI), Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Eva Lucía Margarita Figuerola
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina; Instituto de Biociencias, Biotecnología y Biología Traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Luis Gabriel Wall
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina; Laboratorio de Bioquímica y Biología de Suelos, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes (UNQ), Bernal, Buenos Aires, Argentina
| | - Julieta Mariana Covelli
- Laboratorio de Bioquímica y Biología de Suelos, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes (UNQ), Bernal, Buenos Aires, Argentina
| | - Ana Carolina Agnello
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, CONICET-UNLP), La Plata, Argentina
| | - Esteban Emanuel Nieto
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, CONICET-UNLP), La Plata, Argentina
| | - Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, CONICET-UNLP), La Plata, Argentina
| | - Lina Edith Dominici
- Centro de Investigación y Desarrollo en Tecnología de Pinturas y Recubrimientos (CIDEPINT, CICPBA-CONICET-UNLP), La Plata, Argentina
| | - Marco Allegrini
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS, CONICET-UNS), Bahía Blanca, Buenos Aires, Argentina
| | - María Celina Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS, CONICET-UNS), Bahía Blanca, Buenos Aires, Argentina; Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Marianela Estefanía Morales
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS, CONICET-UNS), Bahía Blanca, Buenos Aires, Argentina; Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, 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 'Dr Héctor Maldonado', Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Anahi Coniglio
- Laboratorio de Fisiología Vegetal y de la Interacción Planta Microorganismo (LFVIPM), Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba, Argentina
| | - Fabricio Dario Cassán
- Laboratorio de Fisiología Vegetal y de la Interacción Planta Microorganismo (LFVIPM), Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba, Argentina
| | - Sofia Nievas
- Laboratorio de Fisiología Vegetal y de la Interacción Planta Microorganismo (LFVIPM), Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba, Argentina
| | - Diego M Roldán
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Ministerio de Educación y Cultura, Montevideo, Uruguay; Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Rodolfo Menes
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay; Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Patricia Vaz Jauri
- Laboratorio de Microbiología de Suelos, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay; Laboratorio de Interacción Planta-Microorganismo, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Carla Silva Marrero
- Laboratorio de Microbiología de Suelos, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Adriana Montañez Massa
- Laboratorio de Microbiología de Suelos, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - María Adelina Morel Revetria
- Laboratorio de Microbiología de Suelos, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay; Laboratorio de Microbiología Molecular, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Ana Fernández-Scavino
- Laboratorio de Ecología Microbiana y Microbiología Ambiental, Departamento de Biociencias, Facultad de Química, Universidad de la República (UdelarR), Montevideo, Uruguay
| | - Luciana Pereira-Mora
- Laboratorio de Ecología Microbiana y Microbiología Ambiental, Departamento de Biociencias, Facultad de Química, Universidad de la República (UdelarR), Montevideo, Uruguay
| | - Soledad Martínez
- Laboratorio de Biotecnología, Departamento de Biociencias, Unidad de Análisis de Agua, Facultad de Química, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Juan Pablo Frene
- School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
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Fonseca A, Kenney S, Van Syoc E, Bierly S, Dini-Andreote F, Silverman J, Boney J, Ganda E. Investigating antibiotic free feed additives for growth promotion in poultry: effects on performance and microbiota. Poult Sci 2024; 103:103604. [PMID: 38484563 PMCID: PMC10951610 DOI: 10.1016/j.psj.2024.103604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/24/2024] Open
Abstract
The poultry industry is evolving towards antibiotic-free production to meet market demands and decelerate the increasing spread of the antimicrobial resistance. The growing need for antibiotic free products has challenged producers to decrease or completely stop using antimicrobials as feed supplements in broiler diet to improve feed efficiency, growth rate, and intestinal health. Natural feed additives (e.g., probiotics and phytobiotics) are promising alternatives to substitute antimicrobial growth promoters. The goal of our study was to characterize the effects of a Probiotic and an Essential Oils blend on broilers' performance and perform a time-series analysis to describe their excreta microbiome. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 d in 32 randomly allocated cages. Treatments consisted of 4 experimental diets: a basal diet, and a basal diet mixed with an Antibiotic (bacitracin methylene disalicylate), an essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Body weight (on 1, 10, and 21d), and feed intake (10d and 21d) were recorded and feed conversion ratio was calculated. Droppings were collected daily (1-21d) to characterize broilers' excreta microbiota by targeted sequencing of the bacterial 16S rRNA gene. The Probiotic significantly improved feed conversion ratio for starter phase 1 to 10d (P = 0.03), grower phase 10 to 21d (P = 0.05), and total period 1 to 21d (P = 0.01) compared to the Antibiotic. Feed supplements did not affect alpha diversity but did impact microbial beta diversity (P < 0.01). Age also impacted microbiome turnover as differences in alpha and beta diversity were detected. Furthermore, when compared to the basal diet, the probiotic and antibiotic significantly impacted relative abundance of Bifidobacterium (log2 fold change -1.44, P = 0.03), Intestinimonas (log2 fold change 0.560, P < 0.01) and Ligilactobacillus (log2 fold change -1.600, P < 0.01). Overall, Probiotic supplementation but not essential oils supplementation positively impacted broilers' growth performance by directly causing directional shifts in broilers' excreta microbiota structure.
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Affiliation(s)
- Ana Fonseca
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA
| | - Sophia Kenney
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA
| | - Emily Van Syoc
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA; Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Stephanie Bierly
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA
| | - Francisco Dini-Andreote
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA; Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Justin Silverman
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA; College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA, USA; Department of Statistics, The Pennsylvania State University, University Park, PA, USA; Department of Medicine, The Pennsylvania State University, University Park, PA, USA; Institute for Computational and Data Science, The Pennsylvania State University, University Park, PA, USA
| | - John Boney
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
| | - Erika Ganda
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA.
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86
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Tokash-Peters AG, Niyonzima JD, Kayirangwa M, Muhayimana S, Tokash IW, Jabon JD, Lopez SG, Kearns PJ, Woodhams DC. Mosquito Microbiomes of Rwanda: Characterizing Mosquito Host and Microbial Communities in the Land of a Thousand Hills. MICROBIAL ECOLOGY 2024; 87:64. [PMID: 38691215 PMCID: PMC11062966 DOI: 10.1007/s00248-024-02382-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/18/2024] [Indexed: 05/03/2024]
Abstract
Mosquitoes are a complex nuisance around the world and tropical countries bear the brunt of the burden of mosquito-borne diseases. Rwanda has had success in reducing malaria and some arboviral diseases over the last few years, but still faces challenges to elimination. By building our understanding of in situ mosquito communities in Rwanda at a disturbed, human-occupied site and at a natural, preserved site, we can build our understanding of natural mosquito microbiomes toward the goal of implementing novel microbial control methods. Here, we examined the composition of collected mosquitoes and their microbiomes at two diverse sites using Cytochrome c Oxidase I sequencing and 16S V4 high-throughput sequencing. The majority (36 of 40 species) of mosquitoes captured and characterized in this study are the first-known record of their species for Rwanda but have been characterized in other nations in East Africa. We found significant differences among mosquito genera and among species, but not between mosquito sexes or catch method. Bacteria of interest for arbovirus control, Asaia, Serratia, and Wolbachia, were found in abundance at both sites and varied greatly by species.
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Affiliation(s)
- Amanda G Tokash-Peters
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
- Center of Excellence in Biodiversity, University of Rwanda, Huye, Rwanda
| | | | | | - Simon Muhayimana
- Center of Excellence in Biodiversity, University of Rwanda, Huye, Rwanda
| | - Ivan W Tokash
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Jaimy D Jabon
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Sergio G Lopez
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Patrick J Kearns
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Douglas C Woodhams
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA.
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87
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Zhu X, Li P, Ju F. Microbiome dynamics and products profiles of biowaste fermentation under different organic loads and additives. Eng Life Sci 2024; 24:2300216. [PMID: 38708413 PMCID: PMC11065332 DOI: 10.1002/elsc.202300216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/26/2023] [Accepted: 10/05/2023] [Indexed: 05/07/2024] Open
Abstract
Biowaste fermentation is a promising technology for low-carbon print bioenergy and biochemical production. Although it is believed that the microbiome determines both the fermentation efficiency and the product profiles of biowastes, the explicit mechanisms of how microbial activity controls fermentation processes remained to be unexplored. The current study investigated the microbiome dynamics and fermentation product profiles of biowaste fermentation under different organic loads (5, 20, and 40 g-VS/L) and with additives that potentially modulate the fermentation process via methanogenesis inhibition (2-bromoethanesulfonate) or electron transfer promotion (i.e., reduced iron, magnetite iron, and activated carbon). The overall fermentation products yields were 440, 373 and 208 CH4-eq/g-VS for low-, medium- and high-load fermentation. For low- and medium-load fermentation, volatile fatty acids (VFAs) were first accumulated and were gradually converted to methane. For high-load fermentation, VFAs were the main fermentation products during the entire fermentation period, accounting for 62% of all products. 16S rRNA-based analyses showed that both 2-bromoethanesulfonate addition and increase of organic loads inhibited the activity of methanogens and promoted the activity of distinct VFA-producing bacterial microbiomes. Moreover, the addition of activated carbon promoted the activity of H2-producing Bacteroides, homoacetogenic Eubacteriaceae and methanogenic Methanosarcinaceae, whose activity dynamics during the fermentation led to changes in acetate and methane production. The current results unveiled mechanisms of microbiome activity dynamics shaping the biowaste fermentation product profiles and provided the fundamental basis for the development of microbiome-guided engineering approaches to modulate biowaste fermentation toward high-value product recovery.
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Affiliation(s)
- Xinyu Zhu
- Key Laboratory of Coastal Environment and Resources of Zhejiang ProvinceSchool of EngineeringWestlake UniversityHangzhouZhejiang ProvinceChina
- Environmental Microbiome and Biotechnology Laboratory, Center of Synthetic Biology and Integrated BioengineeringWestlake UniversityHangzhouZhejiang ProvinceChina
- Institute of Advanced TechnologyWestlake Institute for Advanced StudyHangzhouZhejiang ProvinceChina
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
| | - Ping Li
- Key Laboratory of Coastal Environment and Resources of Zhejiang ProvinceSchool of EngineeringWestlake UniversityHangzhouZhejiang ProvinceChina
- Environmental Microbiome and Biotechnology Laboratory, Center of Synthetic Biology and Integrated BioengineeringWestlake UniversityHangzhouZhejiang ProvinceChina
- Institute of Advanced TechnologyWestlake Institute for Advanced StudyHangzhouZhejiang ProvinceChina
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang ProvinceSchool of EngineeringWestlake UniversityHangzhouZhejiang ProvinceChina
- Environmental Microbiome and Biotechnology Laboratory, Center of Synthetic Biology and Integrated BioengineeringWestlake UniversityHangzhouZhejiang ProvinceChina
- Institute of Advanced TechnologyWestlake Institute for Advanced StudyHangzhouZhejiang ProvinceChina
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
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88
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Usyk M, Hayes RB, Knight R, Gonzalez A, Li H, Osman I, Weber JS, Ahn J. Gut microbiome is associated with recurrence-free survival in patients with resected Stage IIIB-D or Stage IV melanoma treated with immune checkpoint inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589761. [PMID: 38659744 PMCID: PMC11042335 DOI: 10.1101/2024.04.16.589761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The gut microbiome (GMB) has been associated with outcomes of immune checkpoint blockade therapy in melanoma, but there is limited consensus on the specific taxa involved, particularly across different geographic regions. We analyzed pre-treatment stool samples from 674 melanoma patients participating in a phase-III trial of adjuvant nivolumab plus ipilimumab versus nivolumab, across three continents and five regions. Longitudinal analysis revealed that GMB was largely unchanged following treatment, offering promise for lasting GMB-based interventions. In region-specific and cross-region meta-analyses, we identified pre-treatment taxonomic markers associated with recurrence, including Eubacterium, Ruminococcus, Firmicutes, and Clostridium. Recurrence prediction by these markers was best achieved across regions by matching participants on GMB compositional similarity between the intra-regional discovery and external validation sets. AUCs for prediction ranged from 0.83-0.94 (depending on the initial discovery region) for patients closely matched on GMB composition (e.g., JSD ≤0.11). This evidence indicates that taxonomic markers for prediction of recurrence are generalizable across regions, for individuals of similar GMB composition.
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Affiliation(s)
- Mykhaylo Usyk
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Richard B. Hayes
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Rob Knight
- Departments of Pediatrics, Computer Science & Engineering, and Bioengineering; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Antonio Gonzalez
- Departments of Pediatrics, Computer Science & Engineering, and Bioengineering; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Huilin Li
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Iman Osman
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
- The Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Jeffrey S. Weber
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Jiyoung Ahn
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
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89
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Kruger BR, Sackett JD. Abiotic and biotic factors influencing small-scale corn production along a shade spectrum in arid urban agriculture settings. PLoS One 2024; 19:e0301633. [PMID: 38625854 PMCID: PMC11020971 DOI: 10.1371/journal.pone.0301633] [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: 08/24/2023] [Accepted: 03/19/2024] [Indexed: 04/18/2024] Open
Abstract
Urban agriculture may be an avenue to help alleviate strain on the global production of staple crops like corn (Zea mays), but significant knowledge gaps exist regarding the optimization of staple crop production in urban settings, and especially in arid urban settings where different challenges exist for crop success. We sought to assess abiotic and biotic factors that impact sweet corn production in six arid urban agricultural plots with varying levels of shade stress, a known inhibitor of corn production. Corn successfully reached maturity in 50% of the studied plots (n = 18). Microbial richness and diversity were uniformly high in all plot soils and not indicated as a hinderance to corn production nor correlated with corn success. Multiple corn success metrics were positively correlated with average daytime light intensity (r = 0.74 to 0.84) and soil organic matter (r = 0.77 to 0.89), suggesting that these factors are critical aspects of successful corn production. In plots that did not receive optimal light exposure, exceptional soil health and morning vs afternoon sun exposure offset at least some degree of shade stress in these arid urban environments. Corn success metrics were negatively correlated with soil calcium, magnesium, sodium and sulfate (r = -0.71 to -0.90), suggesting that minimizing or mitigating the buildup of salt constituents in soils is critical for successful corn production. Optimizing staple crop production in arid urban agricultural settings supports food chain stability and social and economic security of local communities. This work suggests abiotic and biotic drivers of corn success which can be utilized for crop optimization in these environments.
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Affiliation(s)
- Brittany R. Kruger
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, Nevada, United States of America
| | - Joshua D. Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
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90
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Li XM, Hu HF, Chen SC. Artificial light at night causes community instability of bacterial community in urban soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171129. [PMID: 38395158 DOI: 10.1016/j.scitotenv.2024.171129] [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: 10/02/2023] [Revised: 01/16/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
Abstract
Urban soils host diverse bacteria crucial for ecosystem functions and urban health. As urbanization rises, artificial light at night (ALAN) imposes disturbances on soil ecosystems, yet how ALAN affects the structure and stability of soil bacterial community remains unclear. Here we coupled a short-term incubation experiment, community profiling, network analysis, and in situ field survey to assess the ecological impacts of ALAN. We showed that ALAN influenced bacterial compositions and shifted the bacterial network to a less stable phase, altering denitrification potential. Such transition in community stability probably resulted from an ALAN-induced decrease in competition and/or an increase in facilitation, in line with the Stress Gradient Hypothesis. Similar destabilizing effects were also detected in bacterial networks in multiple urban soils subjected to different levels of ALAN stress, supporting the action of ALAN on naturally-occurring soil bacterial communities. Overall, our findings highlight ALAN as a new form of anthropogenic stress that jeopardizes the stability of soil bacterial community, which would facilitate ecological projection of expanding ALAN exposure.
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Affiliation(s)
- Xiao-Min Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Peoples R China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, Peoples R China; Division of Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria.
| | - Hui-Feng Hu
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria; Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna 1010, Austria
| | - Song-Can Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria.
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91
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Shterzer N, Sbehat Y, Poudel B, Rothschild N, Oloko OE, Druyan S, Mills E. Comparative analysis of reproductive tract microbiomes in modern and slower-growing broiler breeder lines. Front Vet Sci 2024; 11:1386410. [PMID: 38659448 PMCID: PMC11039882 DOI: 10.3389/fvets.2024.1386410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction The reproductive tract microbiome in hens is of interest because bacteria in the reproductive tract could potentially affect fertilization and egg production, as well as integrate into the forming egg and vertically transmit to progeny. Methods The reproductive tract microbiome of 37-week-old modern commercial Cobb breeding dams was compared with that of dams from a broiler Legacy line which has not undergone selection since 1986. All animals were kept together under the same management protocol from day of hatch to avoid confounders. Results In regards to reproductive abilities, Cobb dams' eggs weighed more and the magnum section of their reproductive tract was longer. In regards to microbiome composition, it was found that the reproductive tract microbiomes of the two lines had a lot in common but also that the two breeds have unique reproductive tract microbiomes. Specifically, the order Pseudomonadales was higher in the magnum of Legacy dams, while Verrucomicrobiales was lower. In the infundibulum, Lactobacillales were higher in the Legacy dams while Verrucomicrobiales, Bacteroidales, RF32 and YS2 were lower. Discussion our results show that breeding programs have modified not only the physiology of the reproductive tract but also the reproductive tract microbiome. Additional research is required to understand the implications of these changes in the reproductive tract microbiome on the chicken host.
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Affiliation(s)
- Naama Shterzer
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yara Sbehat
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Binita Poudel
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Nir Rothschild
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Olanrewaju Eunice Oloko
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- Department of Poultry and Aquaculture Science, Agricultural Research Organization, Volcani Center, Rishon LeTsiyon, Israel
| | - Shelly Druyan
- Department of Poultry and Aquaculture Science, Agricultural Research Organization, Volcani Center, Rishon LeTsiyon, Israel
| | - Erez Mills
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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92
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Jensen TBN, Dall SM, Knutsson S, Karst SM, Albertsen M. High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing. PLoS One 2024; 19:e0301446. [PMID: 38573983 PMCID: PMC10994328 DOI: 10.1371/journal.pone.0301446] [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: 09/05/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large sequencing projects are now hampered by the cost of library preparation and low sample throughput, comparatively to the actual sequencing costs. Here, we benchmarked three high-throughput DNA extraction methods: ZymoBIOMICS™ 96 MagBead DNA Kit, MP BiomedicalsTM FastDNATM-96 Soil Microbe DNA Kit, and DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit. The DNA extractions were evaluated based on length, quality, quantity, and the observed microbial community across five diverse soil types. DNA extraction of all soil types was successful for all kits, however DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit excelled across all performance parameters. We further used the nanoliter dispensing system I.DOT One to miniaturize Illumina amplicon and metagenomic library preparation volumes by a factor of 5 and 10, respectively, with no significant impact on the observed microbial communities. With these protocols, DNA extraction, metagenomic, or amplicon library preparation for one 96-well plate are approx. 3, 5, and 6 hours, respectively. Furthermore, the miniaturization of amplicon and metagenome library preparation reduces the chemical and plastic costs from 5.0 to 3.6 and 59 to 7.3 USD pr. sample. This enhanced efficiency and cost-effectiveness will enable researchers to undertake studies with greater sample sizes and diversity, thereby providing a richer, more detailed view of microbial communities and their dynamics.
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Affiliation(s)
- Thomas Bygh Nymann Jensen
- Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sebastian Mølvang Dall
- Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Knutsson
- Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Søren Michael Karst
- Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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93
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Das Baksi K, Pokhrel V, Pudavar AE, Mande SS, Kuntal BK. BactInt: A domain driven transfer learning approach for extracting inter-bacterial associations from biomedical text. Comput Biol Chem 2024; 109:108012. [PMID: 38198963 DOI: 10.1016/j.compbiolchem.2023.108012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/15/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND The healthy as well as dysbiotic state of an ecosystem like human body is known to be influenced not only by the presence of the bacterial groups in it, but also with respect to the associations within themselves. Evidence reported in biomedical text serves as a reliable source for identifying and ascertaining such inter bacterial associations. However, the complexity of the reported text as well as the ever-increasing volume of information necessitates development of methods for automated and accurate extraction of such knowledge. METHODS A BioBERT (biomedical domain specific language model) based information extraction model for bacterial associations is presented that utilizes learning patterns from other publicly available datasets. Additionally, a specialized sentence corpus has been developed to significantly improve the prediction accuracy of the 'transfer learned' model using a fine-tuning approach. RESULTS The final model was seen to outperform all other variations (non-transfer learned and non-fine-tuned models) as well as models trained on BioGPT (a domain trained Generative Pre-trained Transformer). To further demonstrate the utility, a case study was performed using bacterial association network data obtained from experimental studies. CONCLUSION This study attempts to demonstrate the applicability of transfer learning in a niche field of life sciences where understanding of inter bacterial relationships is crucial to obtain meaningful insights in comprehending microbial community structures across different ecosystems. The study further discusses how such a model can be further improved by fine tuning using limited training data. The results presented and the datasets made available are expected to be a valuable addition in the field of medical informatics and bioinformatics.
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Affiliation(s)
| | - Vatsala Pokhrel
- TCS Research, Tata Consultancy Services Ltd, Pune 411057, India
| | | | | | - Bhusan K Kuntal
- TCS Research, Tata Consultancy Services Ltd, Pune 411057, India.
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94
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Welsh BL, Eisenhofer R. The prevalence of controls in phyllosphere microbiome research: a methodological review. THE NEW PHYTOLOGIST 2024; 242:23-29. [PMID: 38339825 DOI: 10.1111/nph.19573] [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: 09/07/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
DNA contamination can critically confound microbiome studies. Here, we take a systematic approach to review the current literature and investigate the prevalence of contamination controls in phyllosphere microbiome research over the past decade. By utilising systematic review principles for this review, we were able to conduct a thorough investigation, screening 450 articles from three databases for eligibility and extracting data in a controlled and methodical manner. Worryingly, we observed a surprisingly low usage of both positive and negative contamination controls in phyllosphere research. As a result, we propose a set of minimum standards to combat the effects of contamination in future phyllosphere research.
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Affiliation(s)
- Brady L Welsh
- School of Biological Sciences, The University of Adelaide, North Terrace Campus, Adelaide, SA, 5005, Australia
| | - Raphael Eisenhofer
- School of Biological Sciences, The University of Adelaide, North Terrace Campus, Adelaide, SA, 5005, Australia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, 1353, Denmark
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95
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Bornbusch SL, Power ML, Schulkin J, Drea CM, Maslanka MT, Muletz-Wolz CR. Integrating microbiome science and evolutionary medicine into animal health and conservation. Biol Rev Camb Philos Soc 2024; 99:458-477. [PMID: 37956701 DOI: 10.1111/brv.13030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data.
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Affiliation(s)
- Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Michael L Power
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Jay Schulkin
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, 1959 NE Pacific St., Box 356460, Seattle, WA, 98195, USA
| | - Christine M Drea
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences, Campus Box 90383, Durham, NC, 27708, USA
| | - Michael T Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
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96
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Scott SA, Fu J, Chang PV. Dopamine receptor D2 confers colonization resistance via microbial metabolites. Nature 2024; 628:180-185. [PMID: 38480886 PMCID: PMC11097147 DOI: 10.1038/s41586-024-07179-5] [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: 09/13/2021] [Accepted: 02/07/2024] [Indexed: 03/26/2024]
Abstract
The gut microbiome has major roles in modulating host physiology. One such function is colonization resistance, or the ability of the microbial collective to protect the host against enteric pathogens1-3, including enterohaemorrhagic Escherichia coli (EHEC) serotype O157:H7, an attaching and effacing (AE) food-borne pathogen that causes severe gastroenteritis, enterocolitis, bloody diarrhea and acute renal failure4,5 (haemolytic uremic syndrome). Although gut microorganisms can provide colonization resistance by outcompeting some pathogens or modulating host defence provided by the gut barrier and intestinal immune cells6,7, this phenomenon remains poorly understood. Here, we show that activation of the neurotransmitter receptor dopamine receptor D2 (DRD2) in the intestinal epithelium by gut microbial metabolites produced upon dietary supplementation with the essential amino acid L-tryptophan protects the host against Citrobacter rodentium, a mouse AE pathogen that is widely used as a model for EHEC infection8,9. We further find that DRD2 activation by these tryptophan-derived metabolites decreases expression of a host actin regulatory protein involved in C. rodentium and EHEC attachment to the gut epithelium via formation of actin pedestals. Our results reveal a noncanonical colonization resistance pathway against AE pathogens that features an unconventional role for DRD2 outside the nervous system in controlling actin cytoskeletal organization in the gut epithelium. Our findings may inspire prophylactic and therapeutic approaches targeting DRD2 with dietary or pharmacological interventions to improve gut health and treat gastrointestinal infections, which afflict millions globally.
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Affiliation(s)
- Samantha A Scott
- Department of Microbiology, Cornell University, Ithaca, NY, USA
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Jingjing Fu
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Pamela V Chang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA.
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
- Cornell Center for Immunology, Cornell University, Ithaca, NY, USA.
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, USA.
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97
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Ma B, Wang Y, Zhao K, Stirling E, Lv X, Yu Y, Hu L, Tang C, Wu C, Dong B, Xue R, Dahlgren RA, Tan X, Dai H, Zhu YG, Chu H, Xu J. Biogeographic patterns and drivers of soil viromes. Nat Ecol Evol 2024; 8:717-728. [PMID: 38383853 DOI: 10.1038/s41559-024-02347-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.
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Affiliation(s)
- Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Yiling Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Erinne Stirling
- Agriculture and Food, CSIRO, Adelaide, South Australia, Australia
- Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, China
| | - Yijun Yu
- Arable Soil Quality and Fertilizer Administration Bureau of Zhejiang Province, Hangzhou, China
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Chao Tang
- Institute of Applied Remote Sensing and Information Technology, Zhejiang University, Hangzhou, China
| | - Chuyi Wu
- School of Earth Sciences, Zhejiang University, Hangzhou, China
| | - Baiyu Dong
- Institute of Applied Remote Sensing and Information Technology, Zhejiang University, Hangzhou, China
| | - Ran Xue
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hengyi Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Yong-Guan Zhu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
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98
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Chao H, Cai A, Heimburger B, Wu Y, Zhao D, Sun M, Hu F. Keystone taxa enhance the stability of soil bacterial communities and multifunctionality under steelworks disturbance. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120664. [PMID: 38508006 DOI: 10.1016/j.jenvman.2024.120664] [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: 12/04/2023] [Revised: 02/19/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Continuous discharge of wastewater, emissions, and solid wastes from steelworks poses environmental risks to ecosystems. However, the role of keystone taxa in maintaining multifunctional stability during environmental disturbances remains poorly understood. To address this, we investigated the community diversity, assembly mechanisms, and soil multifunctionality of soils collected from within the steelworks (I), within 2.5 km radius from the steelworks (E), and from an undisturbed area (CK) in Jiangsu Province, China, via 16 S rRNA sequencing. Significant differences were found in the Chao1 and the richness indexes of the total taxa (p < 0.05), while the diversity of keystone taxa was not significant at each site (p > 0.05). The deterministic processes for total taxa were 42.9%, 61.9% and 47.7% in CK, E, and I, respectively. Steelworks stress increased the deterministicity of keystone taxa from 52.3% in CK to 61.9% in E and I soils. The average multifunctionality indices were 0.518, 0.506 and 0.513 for CK, E and I, respectively. Although the soil multifunctionality was positive correlated with α diversity of both the total and keystone taxa, the average degree of keystone taxa in functional network increased significantly (79.96 and 65.58, respectively), while the average degree of total taxa decreased (44.59 and 51.25, respectively) in the E and I. This suggests keystone taxa contribute to promoting the stability of ecosystems. With increasing disturbance, keystone taxa shift their function from basic metabolism (ribosome biogenesis) to detoxification (xenobiotics biodegradation, metabolism, and benzoate degradation). Here we show that keystone taxa are the most important factor in maintaining stable microbial communities and functions, providing new insights for mitigating pollution stress and soil health protection.
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Affiliation(s)
- Huizhen Chao
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China; J.F. Blumenbach Institute of Zoology and Anthropology, University of Gottingen, Untere Karspule 2, 37073, Gottingen, Germany
| | - Anjuan Cai
- Jiangsu Provincial Academy of Environmental Science, 210019, China
| | - Bastian Heimburger
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Gottingen, Untere Karspule 2, 37073, Gottingen, Germany
| | - Yunling Wu
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Duokai Zhao
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingming Sun
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Feng Hu
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
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99
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Salvadori M, Rosso G. Update on the gut microbiome in health and diseases. World J Methodol 2024; 14:89196. [PMID: 38577200 PMCID: PMC10989414 DOI: 10.5662/wjm.v14.i1.89196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/18/2023] [Accepted: 01/27/2024] [Indexed: 03/07/2024] Open
Abstract
The Human Microbiome Project, Earth Microbiome Project, and next-generation sequencing have advanced novel genome association, host genetic linkages, and pathogen identification. The microbiome is the sum of the microbes, their genetic information, and their ecological niche. This study will describe how millions of bacteria in the gut affect the human body in health and disease. The gut microbiome changes in relation with age, with an increase in Bacteroidetes and Firmicutes. Host and environmental factors affecting the gut microbiome are diet, drugs, age, smoking, exercise, and host genetics. In addition, changes in the gut microbiome may affect the local gut immune system and systemic immune system. In this study, we discuss how the microbiome may affect the metabolism of healthy subjects or may affect the pathogenesis of metabolism-generating metabolic diseases. Due to the high number of publications on the argument, from a methodologically point of view, we decided to select the best papers published in referred journals in the last 3 years. Then we selected the previously published papers. The major goals of our study were to elucidate which microbiome and by which pathways are related to healthy and disease conditions.
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Affiliation(s)
- Maurizio Salvadori
- Department of Renal Transplantation, Careggi University Hospital, Florence 50139, Tuscany, Italy
| | - Giuseppina Rosso
- Division of Nephrology, San Giovanni di Dio Hospital, Florence 50143, Toscana, Italy
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100
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Zeng F, Su X, Liang X, Liao M, Zhong H, Xu J, Gou W, Zhang X, Shen L, Zheng JS, Chen YM. Gut microbiome features and metabolites in non-alcoholic fatty liver disease among community-dwelling middle-aged and older adults. BMC Med 2024; 22:104. [PMID: 38454425 PMCID: PMC10921631 DOI: 10.1186/s12916-024-03317-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND The specific microbiota and associated metabolites linked to non-alcoholic fatty liver disease (NAFLD) are still controversial. Thus, we aimed to understand how the core gut microbiota and metabolites impact NAFLD. METHODS The data for the discovery cohort were collected from the Guangzhou Nutrition and Health Study (GNHS) follow-up conducted between 2014 and 2018. We collected 272 metadata points from 1546 individuals. The metadata were input into four interpretable machine learning models to identify important gut microbiota associated with NAFLD. These models were subsequently applied to two validation cohorts [the internal validation cohort (n = 377), and the prospective validation cohort (n = 749)] to assess generalizability. We constructed an individual microbiome risk score (MRS) based on the identified gut microbiota and conducted animal faecal microbiome transplantation experiment using faecal samples from individuals with different levels of MRS to determine the relationship between MRS and NAFLD. Additionally, we conducted targeted metabolomic sequencing of faecal samples to analyse potential metabolites. RESULTS Among the four machine learning models used, the lightGBM algorithm achieved the best performance. A total of 12 taxa-related features of the microbiota were selected by the lightGBM algorithm and further used to calculate the MRS. Increased MRS was positively associated with the presence of NAFLD, with odds ratio (OR) of 1.86 (1.72, 2.02) per 1-unit increase in MRS. An elevated abundance of the faecal microbiota (f__veillonellaceae) was associated with increased NAFLD risk, whereas f__rikenellaceae, f__barnesiellaceae, and s__adolescentis were associated with a decreased presence of NAFLD. Higher levels of specific gut microbiota-derived metabolites of bile acids (taurocholic acid) might be positively associated with both a higher MRS and NAFLD risk. FMT in mice further confirmed a causal association between a higher MRS and the development of NAFLD. CONCLUSIONS We confirmed that an alteration in the composition of the core gut microbiota might be biologically relevant to NAFLD development. Our work demonstrated the role of the microbiota in the development of NAFLD.
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Affiliation(s)
- Fangfang Zeng
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, No.601 Huangpu Road West, Guangzhou, 510632, China.
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Xin Su
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, No.601 Huangpu Road West, Guangzhou, 510632, China
| | - Xinxiu Liang
- Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, 310030, China
| | - Minqi Liao
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Haili Zhong
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jinjian Xu
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Wanglong Gou
- Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, 310030, China
| | - Xiangzhou Zhang
- Big Data Decision Institute, Jinan University, No.601 Huangpu Road West, Guangzhou, 510632, China
| | - Luqi Shen
- Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, 310030, China
| | - Ju-Sheng Zheng
- Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, 310030, China.
| | - Yu-Ming Chen
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, Guangzhou, 510275, China.
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