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Hu W, Zheng N, Zhang Y, Li S, Bartlam M, Wang Y. Metagenomics analysis reveals effects of salinity fluctuation on diversity and ecological functions of high and low nucleic acid content bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173186. [PMID: 38744390 DOI: 10.1016/j.scitotenv.2024.173186] [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: 03/26/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Salinity is a critical environmental factor in marine ecosystems and has complex and wide-ranging biological effects. However, the effects of changing salinity on diversity and ecological functions of high nucleic acid (HNA) and low nucleic acid (LNA) bacteria are not well understood. In this study, we used 16S rRNA sequencing and metagenomic sequencing analysis to reveal the response of HNA and LNA bacterial communities and their ecological functions to salinity, which was decreased from 26 ‰ to 16 ‰. The results showed that salinity changes had significant effects on the community composition of HNA and LNA bacteria. Among LNA bacteria, 14 classes showed a significant correlation between relative abundance and salinity. Salinity changes can lead to the transfer of some bacteria from HNA bacteria to LNA bacteria. In the network topology relationship, the complexity of the network between HNA and LNA bacterial communities gradually decreased with decreased salinity. The abundance of some carbon and nitrogen cycling genes in HNA and LNA bacteria varied with salinity. Overall, this study demonstrates the effects of salinity on diversity and ecological functions and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions.
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Affiliation(s)
- Wei Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Ningning Zheng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Yi Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Shuhan Li
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China.
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China.
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2
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Yin T, Zhang X, Long Y, Jiang J, Zhou S, Chen Z, Hu J, Ma S. Impact of soil physicochemical factors and heavy metals on co-occurrence pattern of bacterial in rural simple garbage dumping site. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116476. [PMID: 38820822 DOI: 10.1016/j.ecoenv.2024.116476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/02/2024]
Abstract
Rural waste accumulation leads to heavy metal soil pollution, impacting microbial communities. However, knowledge gaps exist regarding the distribution and occurrence patterns of bacterial communities in multi-metal contaminated soil profiles. In this study, high-throughput 16 S rRNA gene sequencing technology was used to explore the response of soil bacterial communities to various heavy metal pollution in rural simple waste dumps in karst areas of Southwest China. The study selected three habitats in the center, edge, and uncontaminated areas of the waste dump to evaluate the main factors driving the change in bacterial community composition. Pollution indices reveal severe contamination across all elements, except for moderately polluted lead (Pb); contamination severity ranks as follows: Mn > Cd > Zn > Cr > Sb > V > Cu > As > Pb. Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteriota predominate, collectively constituting over 60% of the relative abundance. Analysis of Chao and Shannon indices demonstrated that the waste dump center boasted the greatest bacterial richness and diversity. Correlation data indicated a predominant synergistic interaction among the landfill's bacterial community, with a higher number of positive associations (76.4%) compared to negative ones (26.3%). Network complexity was minimal at the dump's edge. RDA analysis showed that Pb(explained:46%) and Mn(explained:21%) were the key factors causing the difference in bacterial community composition in the edge area of the waste dump, and AK(explained:42.1%) and Cd(explained:35.2%) were the key factors in the center of the waste dump. This study provides important information for understanding the distribution patterns, co-occurrence networks, and environmental response mechanisms of bacterial communities in landfill soils under heavy metal stress, which helps guide the formulation of rural waste treatment and soil remediation strategies.
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Affiliation(s)
- Tongyun Yin
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Xiangyu Zhang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Yunchuan Long
- Guizhou Academy of Sciences, Shanxi Road 1, Guiyang 550001, PR China
| | - Juan Jiang
- Guizhou Academy of Sciences, Shanxi Road 1, Guiyang 550001, PR China
| | - Shaoqi Zhou
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, PR China; College of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Center, PR China
| | - Zhengquan Chen
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Jing Hu
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, PR China; Guizhou Jiamu Environmental Protection Technology Co., Ltd, PR China.
| | - Shengming Ma
- Guizhou Jiamu Environmental Protection Technology Co., Ltd, PR China
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Sun QW, Chen JZ, Liao XF, Huang XL, Liu JM. Identification of keystone taxa in rhizosphere microbial communities using different methods and their effects on compounds of the host Cinnamomum migao. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171952. [PMID: 38537823 DOI: 10.1016/j.scitotenv.2024.171952] [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: 09/15/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Exploring keystone taxa affecting microbial community stability and host function is crucial for understanding ecosystem functions. However, identifying keystone taxa from humongous microbial communities remains challenging. We collected 344 rhizosphere and bulk soil samples from the endangered plant C. migao for 2 years consecutively. Used high-throughput sequencing 16S rDNA and ITS to obtain the composition of bacterial and fungal communities. We explored keystone taxa and the applicability and limitations of five methods (SPEC-OCCU, Zi-Pi, Subnetwork, Betweenness, and Module), as well as the impact of microbial community domain, time series, and rhizosphere boundary on the identification of keystone taxa in the communities. Our results showed that the five methods, identified abundant keystone taxa in rhizosphere and bulk soil microbial communities. However, the keystone taxa shared by the rhizosphere and bulk soil microbial communities over time decreased rapidly decrease in the five methods. Among five methods on the identification of keystone taxa in the rhizosphere community, Module identified 113 taxa, SPEC-OCCU identified 17 taxa, Betweenness identified 3 taxa, Subnetwork identified 3 taxa, and Zi-Pi identified 4 taxa. The keystone taxa are mainly conditionally rare taxa, and their ecological functions include chemoheterotrophy, aerobic chemoheterotrophy, nitrate reduction, and anaerobic photoautotrophy. The results of the random forest model and structural equation model predict that keystone taxa Mortierella and Ellin6513 may have an effects on the accumulation of 1, 4, 7, - Cycloundecatriene, 1, 5, 9, 9-tetramethyl-, Z, Z, Z-, beta-copaene, bicyclogermacrene, 1,8-Cineole in C. migao fruits, but their effects still need further evidence. Our study evidence an unstable microbial community in the bulk soil, and the definition of microbial boundary and ecologically functional affected the identification of keystone taxa in the community. Subnetwork and Module are more in line with the definition of keystone taxa in microbial ecosystems in terms of maintaining community stability and hosting function.
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Affiliation(s)
- Qing-Wen Sun
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; Guizhou Province Key Laboratory of Chinese Pharmacology and Pharmacognosy, 550025, China
| | - Jing-Zhong Chen
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; Guizhou Province Key Laboratory of Chinese Pharmacology and Pharmacognosy, 550025, China.
| | | | | | - Ji-Ming Liu
- College of Forestry, Guizhou University, Guiyang 550025, China
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Daniel BBJ, Steiger Y, Sintsova A, Field CM, Nguyen BD, Schubert C, Cherrak Y, Sunagawa S, Hardt WD, Vorholt JA. Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags. Nat Microbiol 2024; 9:1103-1116. [PMID: 38503975 PMCID: PMC10994841 DOI: 10.1038/s41564-024-01634-9] [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: 09/19/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024]
Abstract
Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that require intrastrain resolution. Here we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative polymerase chain reaction and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed that they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intrastrain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the Arabidopsis phyllosphere, both with and without microbiota context. We observed colonization resistance against late-arriving strains of Salmonella Typhimurium in the mouse gut, whereas the phyllosphere accommodated Sphingomonas latecomers in a manner proportional to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems.
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Affiliation(s)
| | - Yves Steiger
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Anna Sintsova
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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Zhang Y, Deng Y, Wang C, Li S, Lau FTK, Zhou J, Zhang T. Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants. mSystems 2024; 9:e0133323. [PMID: 38411061 PMCID: PMC10949511 DOI: 10.1128/msystems.01333-23] [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: 12/13/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Wastewater treatment plants (WWTPs) are indispensable biotechnology facilities for modern cities and play an essential role in modern urban infrastructure by employing microorganisms to remove pollutants in wastewater, thus protecting public health and the environment. This study conducted a 13-month bacterial community survey of six full-scale WWTPs in Hong Kong with samples of influent, activated sludge (AS), and effluent to explore their synchronism and asynchronism of bacterial community. Besides, we compared AS results of six Hong Kong WWTPs with data from 1,186 AS amplicon data in 269 global WWTPs and a 9-year metagenomic sequencing survey of a Hong Kong WWTP. Our results showed the compositions of bacterial communities varied and the bacterial community structure of AS had obvious differences across Hong Kong WWTPs. The co-occurrence analysis identified 40 pairs of relationships that existed among Hong Kong WWTPs to show solid associations between two species and stochastic processes took large proportions for the bacterial community assembly of six WWTPs. The abundance and distribution of the functional bacteria in worldwide and Hong Kong WWTPs were examined and compared, and we found that ammonia-oxidizing bacteria had more diversity than nitrite-oxidizing bacteria. Besides, Hong Kong WWTPs could make great contributions to the genome mining of microbial dark matter in the global "wanted list." Operational parameters had important effects on OTUs' abundance, such as the temperature to the genera of Tetrasphaera, Gordonia and Nitrospira. All these results obtained from this study can deepen our understanding of the microbial ecology in WWTPs and provide foundations for further studies. IMPORTANCE Wastewater treatment plants (WWTPs) are an indispensable component of modern cities, as they can remove pollutants in wastewater to prevent anthropogenic activities. Activated sludge (AS) is a fundamental wastewater treatment process and it harbors a highly complex microbial community that forms the main components and contains functional groups. Unveiling "who is there" is a long-term goal of the research on AS microbiology. High-throughput sequencing provides insights into the inventory diversity of microbial communities to an unprecedented level of detail. At present, the analysis of communities in WWTPs usually comes from a specific WWTP and lacks comparisons and verification among different WWTPs. The wide-scale and long-term sampling project and research in this study could help us evaluate the AS community more accurately to find the similarities and different results for different WWTPs in Hong Kong and other regions of the world.
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Affiliation(s)
- Yulin Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Frankie T. K. Lau
- Drainage Services Department, The Government of the Hong Kong Special Administrative Region of the People’s Republic of China, Wanchai, Hong Kong, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
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Wang W, Li L, Ma J. Bioaerosols released from multistage biofilter for gaseous benzene removal: Escape behavior and pathogenicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168817. [PMID: 38029984 DOI: 10.1016/j.scitotenv.2023.168817] [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: 09/12/2023] [Revised: 10/31/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
Biological deodorization systems are widely used to control odors and volatile organic compounds. However, the secondary contamination of bioaerosol emissions is a noteworthy issue in the operation of biofilters for off-gas purification. In this study, a multistage biofilter for benzene treatment was utilized to investigate the bioaerosol emissions under different flow rates and spray intervals. At the outlet of the biofilter, 99-7173 CFU/m3 of bioaerosols were detected, among which pathogens accounted for 8.93-98.73 %. Proteobacteria and Firmicutes dominated bioaerosols at the phylum level. The Mantel test based on the Bray-Curtis distance revealed strong influences of flow rate introduced to the biofilter and biomass colonized on the packing materials (PMs) on bioaerosol emissions. The non-metric multidimensional scaling results suggested a correlation between the bioaerosol community and bacteria on the PMs. Bacillus and Stenotrophomonas were the two main genera stripped from the biofilm on PMs to form the bioaerosols. SourceTracker analysis confirmed that microorganisms from the PMs near outlet contributed an average of 22.3 % to bioaerosols. Pathogenic bacteria carried by bioaerosols included Bacillus, Serratia, Stenotrophomonas, Achromobacter, Enterococcus, and Pseudomonas. Bioaerosols were predicted to cause human diseases, with antimicrobial drug resistance and bacterial infectious disease being the two main pathogenic pathways. Stenotrophomonas sp. LMG 19833, Pseudomonas sp., and Stenotrophomonas sp. were the keystone species in the bioaerosol co-occurrence network. Overall, results of present study promote the insight of bioaerosols, particularly pathogen emissions, and provide a basis for controlling bioaerosol contamination from biofilters.
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Affiliation(s)
- Wenwen Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Lin Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, PR China.
| | - Jiawei Ma
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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Wang H, Xu R, Li Q, Su Y, Zhu W. Daily fluctuation of colonic microbiome in response to nutrient substrates in a pig model. NPJ Biofilms Microbiomes 2023; 9:85. [PMID: 37938228 PMCID: PMC10632506 DOI: 10.1038/s41522-023-00453-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Studies on rodents indicate the daily oscillations of the gut microbiota have biological implications for host. However, the responses of fluctuating gut microbes to the dynamic nutrient substrates are not fully clear. In the study, we found that the feed intake, nutrient substrates, microbiota and metabolites in the colon underwent asynchronous oscillation within a day. Short-chain fatty acids (SCFAs) including acetate, propionate, butyrate and valerate peaked during T24 ~ T27 (Timepoint 24, 12:00 pm, T27, 03:00 am) whereas branched SCFAs isobutyrate and isovalerate peaked during T09 ~ T12. Further extended local similarity analysis (eLSA) revealed that the fluctuation of feed intake dynamically correlated with the colonic carbon substrates which further influenced the oscillation of sugar metabolites and acetate, propionate, butyrate and valerate with a certain time shift. The relative abundance of primary degrader Ruminococcaceae taxa was highly related to the dynamics of the carbon substrates whereas the fluctuations of secondary degraders Lactobacillaceae and Streptococcaceae taxa were highly correlated with the sugar metabolites. Meanwhile, colonic nitrogen substrates were correlated with branched amino acids and the branched SCFAs. Furthermore, we validated the evolution of gut microbes under different carbohydrate and protein combinations by using an in vitro fermentation experiment. The study pictured the dynamics of the micro-ecological environment within a day which highlights the implications of the temporal dimension in studies related to the gut microbiota. Feed intake, more precisely substrate intake, is highly correlated with microbial evolution, which makes it possible to develop chronotherapies targeting the gut microbiota through nutrition intervention.
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Affiliation(s)
- Hongyu Wang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongying Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiuke Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
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Creus-Martí I, Marín-Miret J, Moya A, Santonja FJ. Evidence of the cooperative response of Blattella germanica gut microbiota to antibiotic treatment. Math Biosci 2023; 364:109057. [PMID: 37562583 DOI: 10.1016/j.mbs.2023.109057] [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: 01/24/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023]
Abstract
Gut microbiota plays a key role in host health under normal conditions. However, bacterial composition can be altered by external factors such as antibiotic (AB) intake. While there are many descriptive publications about the effects of AB on gut microbiota composition after treatment, the dynamics and interactions among the bacterial taxa are still poorly understood. In this work, we performed a longitudinal study of gut microbiome dynamics in B. germanica treated with kanamycin. The AB was supplied in three separate periods, giving the microbiota time to recover between each antibiotic intake. We applied two new statistical models, not focusing on pair-wise interactions, to more realistically study the interactions between groups of bacterial taxa and how some groups affect a single taxon. The first model provides information on the importance of a given genus, and the rest of the community, to define the abundance of that genus. The second model, on the other hand, provides details about the relationship between groups of bacteria, focusing on which community groups affect the taxa. These models help us to identify which bacteria are community-dependent in stress conditions, which taxa might be better adapted than the rest of the community, and which bacteria might be working together within the community to overcome the antibiotic. In addition, these models enable us to identify different bacterial groups that were separated in control conditions but were found together in treated conditions, suggesting that when the environment is more hostile (as it is under antibiotic treatment), the whole community tends to work together.
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Affiliation(s)
- Irene Creus-Martí
- Institute for Integrative Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain; Department of Statistics and Operation Research, Universitat de València, Valencia, Spain
| | - Jesús Marín-Miret
- Institute for Integrative Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain; The Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Francisco J Santonja
- Department of Statistics and Operation Research, Universitat de València, Valencia, Spain.
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Regueira-Iglesias A, Balsa-Castro C, Blanco-Pintos T, Tomás I. Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis. Mol Oral Microbiol 2023; 38:347-399. [PMID: 37804481 DOI: 10.1111/omi.12434] [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: 04/26/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them.
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Affiliation(s)
- Alba Regueira-Iglesias
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Carlos Balsa-Castro
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Triana Blanco-Pintos
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Inmaculada Tomás
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
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10
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Xu X, Wang S, Li C, Li J, Gao F, Zheng L. Quorum sensing bacteria in microplastics epiphytic biofilms and their biological characteristics which potentially impact marine ecosystem. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115444. [PMID: 37690175 DOI: 10.1016/j.ecoenv.2023.115444] [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: 04/08/2023] [Revised: 08/24/2023] [Accepted: 09/03/2023] [Indexed: 09/12/2023]
Abstract
Microplastics (MPs) have been shown to be a new type of pollutant in the oceans, with complex biofilms attached to their surfaces. Bacteria with quorum sensing (QS) systems are important participants in biofilms. Such bacteria can secrete and detect signal molecules. When a signal molecule reaches its threshold level, bacteria with QS systems can perform several biological functions, such as biofilm formation and antibiotic metabolite production. However, the ecological effects of QS bacteria in biofilm as MPs distribute globally with ocean currents are not to be elucidate yet. In this study, polypropylene and polyvinyl chloride were selected for on-site enrichment to acquire microplastics with biofilms. Eight culturable QS bacteria in the resulting biofilm were isolated by using biosensor assays, and their biodiversity was analyzed. The profiles of the N-acyl-homoserine lactones (AHLs) produced by these bacteria were analyzed by using thin-layer chromatography (TLC)-bioautography and gas chromatography and mass spectrometry (GC-MS). Biofilm-forming properties and several biological characteristics, such as bacteriostasis, algal inhibition, and dimethylsulfoniopropionate (DMSP) degradation, were explored along with QS quenching. Results showed that QS bacteria were mainly affiliated with class Alphaproteobacteria, particularly Rhodobacteraceae, followed by class Gammaproteobacteria. TLC-bioautography and GC-MS analyses revealed that seven AHLs, namely, C6-HSL, C8-HSL, 3-oxo-C6-HSL, 3-oxo-C8-HSL, 3-oxo-C10-HSL, and two unidentified AHLs were produced. The QS system equipped bacteria with strong biofilm-forming capacity and may contribute to the keystone roles of Rhodobacteraceae. In addition, QS bacteria may exacerbate the adverse environmental effects of MPs, such as inducing the misfeeding of planktons on MPs. This study elucidated the diversity of QS bacteria in MP-associated biofilms and provided a new perspective of the effect of key membrane-forming bacteria on the marine ecological environment.
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Affiliation(s)
- Xiyuan Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Shuai Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Chengxuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Jingxi Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Fenglei Gao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Li Zheng
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory of Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China.
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11
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Ai D, Chen L, Xie J, Cheng L, Zhang F, Luan Y, Li Y, Hou S, Sun F, Xia LC. Identifying local associations in biological time series: algorithms, statistical significance, and applications. Brief Bioinform 2023; 24:bbad390. [PMID: 37930023 DOI: 10.1093/bib/bbad390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/21/2023] [Accepted: 09/14/2023] [Indexed: 11/07/2023] Open
Abstract
Local associations refer to spatial-temporal correlations that emerge from the biological realm, such as time-dependent gene co-expression or seasonal interactions between microbes. One can reveal the intricate dynamics and inherent interactions of biological systems by examining the biological time series data for these associations. To accomplish this goal, local similarity analysis algorithms and statistical methods that facilitate the local alignment of time series and assess the significance of the resulting alignments have been developed. Although these algorithms were initially devised for gene expression analysis from microarrays, they have been adapted and accelerated for multi-omics next generation sequencing datasets, achieving high scientific impact. In this review, we present an overview of the historical developments and recent advances for local similarity analysis algorithms, their statistical properties, and real applications in analyzing biological time series data. The benchmark data and analysis scripts used in this review are freely available at http://github.com/labxscut/lsareview.
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Affiliation(s)
- Dongmei Ai
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Lulu Chen
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Jiemin Xie
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
| | - Longwei Cheng
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Fang Zhang
- Shenwan Hongyuan Securities Co. Ltd., Shanghai 200031, China
| | - Yihui Luan
- School of Mathematics, Shandong University, Jinan 250100, China
| | - Yang Li
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
| | - Shengwei Hou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fengzhu Sun
- Department of Quantitative and Computational Biology, University of Southern California, California, 90007, USA
| | - Li Charlie Xia
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
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12
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Márton Z, Csitári B, Felföldi T, Hidas A, Jordán F, Szabó A, Székely AJ. Contrasting response of microeukaryotic and bacterial communities to the interplay of seasonality and local stressors in shallow soda lakes. FEMS Microbiol Ecol 2023; 99:fiad095. [PMID: 37586889 PMCID: PMC10449373 DOI: 10.1093/femsec/fiad095] [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: 06/19/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
Seasonal environmental variation is a leading driver of microbial planktonic community assembly and interactions. However, departures from usual seasonal trends are often reported. To understand the role of local stressors in modifying seasonal succession, we sampled fortnightly, throughout three seasons, five nearby shallow soda lakes exposed to identical seasonal and meteorological changes. We characterised their microeukaryotic and bacterial communities by amplicon sequencing of the 16S and 18S rRNA gene, respectively. Biological interactions were inferred by analyses of synchronous and time-shifted interaction networks, and the keystone taxa of the communities were topologically identified. The lakes showed similar succession patterns during the study period with spring being characterised by the relevance of trophic interactions and a certain level of community stability followed by a more dynamic and variable summer-autumn period. Adaptation to general seasonal changes happened through shared core microbiome of the lakes. Stochastic events such as desiccation disrupted common network attributes and introduced shifts from the prevalent seasonal trajectory. Our results demonstrated that, despite being extreme and highly variable habitats, shallow soda lakes exhibit certain similarities in the seasonality of their planktonic communities, yet local stressors such as droughts instigate deviations from prevalent trends to a greater extent for microeukaryotic than for bacterial communities.
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Affiliation(s)
- Zsuzsanna Márton
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- National Multidisciplinary Laboratory for Climate Change, Centre for Ecological Research, H-1113 Budapest, Hungary
- Doctoral School of Environmental Sciences, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Bianka Csitári
- Doctoral School of Environmental Sciences, Eötvös Loránd University, H-1117 Budapest, Hungary
- Karolinska Institutet, 171 65 Stockholm, Sweden
- Uppsala University, 752 36 Uppsala, Sweden
| | - Tamás Felföldi
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- Department of Microbiology, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - András Hidas
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- Doctoral School of Environmental Sciences, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Ferenc Jordán
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Attila Szabó
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Anna J Székely
- Uppsala University, 752 36 Uppsala, Sweden
- Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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13
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Wang M, Liu X, Qu L, Wang T, Zhu L, Feng J. Untangling microbiota diversity and assembly patterns in the world's longest underground culvert water diversion canal. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:981. [PMID: 37480396 DOI: 10.1007/s10661-023-11593-z] [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: 04/10/2023] [Accepted: 07/10/2023] [Indexed: 07/24/2023]
Abstract
The long-distance underground box culvert water transport system (LUBWT) is a crucial link between the source of drinking water and the consumers. It must ensure the stability of water quality during transportation. However, uncontrollable microbial growth can develop in the water delivery system during the long delivery process, posing a risk to health and safety. Therefore, we applied 16 s and 18 s gene sequence analysis in order to study microbial communities in box culvert waters sampled in 2021, as well as a molecular ecological network-based approach to decipher microbial interactions and stability. Our findings revealed that, in contrast to natural freshwater ecosystems, micro-eukaryotes in LUBWT have complex interactions such as predation, parasitism, and symbiosis due to their semi-enclosed box culvert environment. Total nitrogen may be the primary factor affecting bacterial community interactions in addition to temperature. Moreover, employing stability indicators such as robustness and vulnerability, we also found that microbial stability varied significantly from season to season, with summer having the higher stability of microbial communities. Not only that but also the stability of the micronuclei also varied greatly during water transport, which might also be related to the complex interactions among the micro-eukaryotes. To summarize, our study reveals the microbial interactions and stability in LUBWT, providing essential ecological knowledge to ensure the safety of LUBWT's water quality.
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Affiliation(s)
- Mengyao Wang
- College of Environmental Science and Engineering, Nankai University, Tianjin, People's Republic of China
| | - Xinyong Liu
- Tianjin Branch of China South to North Water Diversion Middle Route Construction Management Bureau, Tianjin, People's Republic of China.
| | - Liang Qu
- Tianjin Branch of China South to North Water Diversion Middle Route Construction Management Bureau, Tianjin, People's Republic of China
| | - Tongtong Wang
- Tianjin Branch of China South to North Water Diversion Middle Route Construction Management Bureau, Tianjin, People's Republic of China
| | - Lin Zhu
- College of Environmental Science and Engineering, Nankai University, Tianjin, People's Republic of China
| | - Jianfeng Feng
- College of Environmental Science and Engineering, Nankai University, Tianjin, People's Republic of China.
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14
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Aldirawi H, Morales FG. Univariate and Multivariate Statistical Analysis of Microbiome Data: An Overview. Appl Microbiol 2023. [DOI: 10.3390/applmicrobiol3020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Microbiome data is high dimensional, sparse, compositional, and over-dispersed. Therefore, modeling microbiome data is very challenging and it is an active research area. Microbiome analysis has become a progressing area of research as microorganisms constitute a large part of life. Since many methods of microbiome data analysis have been presented, this review summarizes the challenges, methods used, and the advantages and disadvantages of those methods, to serve as an updated guide for those in the field. This review also compared different methods of analysis to progress the development of newer methods.
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15
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Abad N, Uranga A, Ayo B, Arrieta JM, Baña Z, Azúa I, Artolozaga I, Iriberri J, González-Rojí SJ, Unanue M. Kinetic modulation of bacterial hydrolases by microbial community structure in coastal waters. Environ Microbiol 2023; 25:548-561. [PMID: 36478509 PMCID: PMC10108013 DOI: 10.1111/1462-2920.16297] [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: 07/27/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
In this study, we hypothesized that shifts in the kinetic parameters of extracellular hydrolytic enzymes may occur as a consequence of seasonal environmental disturbances and would reflect the level of adaptation of the bacterial community to the organic matter of the ecosystem. We measured the activities of enzymes that play a key role in the bacterial growth (leucine aminopeptidase, β- and α-glucosidases) in surface coastal waters of the Eastern Cantabrian Sea and determined their kinetic parameters by computing kinetic models of distinct complexity. Our results revealed the existence of two clearly distinct enzymatic systems operating at different substrate concentrations: a high-affinity system prevailing at low substrate concentrations and a low-affinity system characteristic of high substrate concentrations. These findings could be the result of distinct functional bacterial assemblages growing concurrently under sharp gradients of high-molecular-weight compounds. We constructed an ecological network based on contemporaneous and time-delayed correlations to explore the associations between the kinetic parameters and the environmental variables. The analysis revealed that the recurring phytoplankton blooms registered throughout the seasonal cycle trigger the wax and wane of those members of the bacterial community able to synthesize and secrete specific enzymes.
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Affiliation(s)
- Naiara Abad
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
- Department of Zoology and Animal Cell Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Alava, Spain
| | - Ainhoa Uranga
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
| | - Begoña Ayo
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | - Jesús Maria Arrieta
- Canary Islands Oceanographic Center, Spanish Institute of Oceanography (IEO-CSIC), Santa Cruz, Spain
| | - Zuriñe Baña
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | - Iñigo Azúa
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | - Itxaso Artolozaga
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
| | - Juan Iriberri
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | - Santos J González-Rojí
- Oeschger Centre for Climate Change Research (OCCR), University of Bern, Bern, Switzerland
- Climate and Environmental Physics (CEP), University of Bern, Bern, Switzerland
| | - Marian Unanue
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
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16
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Scarsella E, Jha A, Sandri M, Stefanon B. Network-based gut microbiome analysis in dogs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2124932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Elisa Scarsella
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Aashish Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Misa Sandri
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Bruno Stefanon
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, University of Udine, Udine, Italy
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17
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Olivença DV, Davis JD, Voit EO. Inference of dynamic interaction networks: A comparison between Lotka-Volterra and multivariate autoregressive models. FRONTIERS IN BIOINFORMATICS 2022; 2:1021838. [PMID: 36619477 PMCID: PMC9815445 DOI: 10.3389/fbinf.2022.1021838] [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: 08/17/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Networks are ubiquitous throughout biology, spanning the entire range from molecules to food webs and global environmental systems. Yet, despite substantial efforts by the scientific community, the inference of these networks from data still presents a problem that is unsolved in general. One frequent strategy of addressing the structure of networks is the assumption that the interactions among molecular or organismal populations are static and correlative. While often successful, these static methods are no panacea. They usually ignore the asymmetry of relationships between two species and inferences become more challenging if the network nodes represent dynamically changing quantities. Overcoming these challenges, two very different network inference approaches have been proposed in the literature: Lotka-Volterra (LV) models and Multivariate Autoregressive (MAR) models. These models are computational frameworks with different mathematical structures which, nevertheless, have both been proposed for the same purpose of inferring the interactions within coexisting population networks from observed time-series data. Here, we assess these dynamic network inference methods for the first time in a side-by-side comparison, using both synthetically generated and ecological datasets. Multivariate Autoregressive and Lotka-Volterra models are mathematically equivalent at the steady state, but the results of our comparison suggest that Lotka-Volterra models are generally superior in capturing the dynamics of networks with non-linear dynamics, whereas Multivariate Autoregressive models are better suited for analyses of networks of populations with process noise and close-to linear behavior. To the best of our knowledge, this is the first study comparing LV and MAR approaches. Both frameworks are valuable tools that address slightly different aspects of dynamic networks.
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18
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Selection pressure on the rhizosphere microbiome can alter nitrogen use efficiency and seed yield in Brassica rapa. Commun Biol 2022; 5:959. [PMID: 36104398 PMCID: PMC9474469 DOI: 10.1038/s42003-022-03860-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 08/18/2022] [Indexed: 01/03/2023] Open
Abstract
AbstractMicrobial experimental systems provide a platform to observe how networks of groups emerge to impact plant development. We applied selection pressure for microbiome enhancement of Brassica rapa biomass to examine adaptive bacterial group dynamics under soil nitrogen limitation. In the 9th and final generation of the experiment, selection pressure enhanced B. rapa seed yield and nitrogen use efficiency compared to our control treatment, with no effect between the random selection and control treatments. Aboveground biomass increased for both the high biomass selection and random selection plants. Soil bacterial diversity declined under high B. rapa biomass selection, suggesting a possible ecological filtering mechanism to remove bacterial taxa. Distinct sub-groups of interactions emerged among bacterial phyla such as Proteobacteria and Bacteroidetes in response to selection. Extended Local Similarity Analysis and NetShift indicated greater connectivity of the bacterial community, with more edges, shorter path lengths, and altered modularity through the course of selection for enhanced plant biomass. In contrast, bacterial communities under random selection and no selection showed less complex interaction profiles of bacterial taxa. These results suggest that group-level bacterial interactions could be modified to collectively shift microbiome functions impacting the growth of the host plant under soil nitrogen limitation.
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19
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Yuan AE, Shou W. Data-driven causal analysis of observational biological time series. eLife 2022; 11:72518. [PMID: 35983746 PMCID: PMC9391047 DOI: 10.7554/elife.72518] [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: 08/09/2021] [Accepted: 01/23/2022] [Indexed: 11/28/2022] Open
Abstract
Complex systems are challenging to understand, especially when they defy manipulative experiments for practical or ethical reasons. Several fields have developed parallel approaches to infer causal relations from observational time series. Yet, these methods are easy to misunderstand and often controversial. Here, we provide an accessible and critical review of three statistical causal discovery approaches (pairwise correlation, Granger causality, and state space reconstruction), using examples inspired by ecological processes. For each approach, we ask what it tests for, what causal statement it might imply, and when it could lead us astray. We devise new ways of visualizing key concepts, describe some novel pathologies of existing methods, and point out how so-called ‘model-free’ causality tests are not assumption-free. We hope that our synthesis will facilitate thoughtful application of methods, promote communication across different fields, and encourage explicit statements of assumptions. A video walkthrough is available (Video 1 or https://youtu.be/AlV0ttQrjK8).
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Affiliation(s)
- Alex Eric Yuan
- Molecular and Cellular Biology PhD program, University of Washington, Seattle, United States.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Wenying Shou
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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20
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Yuan S, Guo S, Huang X, Meng F. Time-lagged interspecies interactions prevail during biofilm development in moving bed biofilm reactor. Biotechnol Bioeng 2022; 119:2770-2783. [PMID: 35837838 DOI: 10.1002/bit.28177] [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: 02/16/2022] [Revised: 06/27/2022] [Accepted: 07/10/2022] [Indexed: 11/09/2022]
Abstract
Clarifying the essential succession dynamics of interspecies interactions during biofilm development is crucial for the regulation and application of biofilm-based processes. In this study, regular and time-series phylogenetic molecular ecological networks (pMENs) were constructed to investigate ordinary and time-lagged interspecies interactions during biofilm development in a moving bed biofilm reactor (MBBR). Positive interactions dominated both regular (89.78%) and time-series (77.04%) ecological networks, suggesting that extensive cooperative behaviors facilitated biofilm development. The pronounced directional interactions (72.52%) in the time-series network further indicated that time-lagged interspecies interactions prevailed in the biofilm development process. Specifically, the proportion of directional negative interactions was higher than that of positive interactions, implying that interspecific competition preferred to be time-lagged. The time-series network revealed that module hubs exhibited extensive time-lagged positive interactions with their neighbors, and most of them exhibited altruistic behaviors. Keystone species possessing more positive interactions were positively correlated with biofilm biomass, NO3 - -N concentrations, and the removal efficiencies of NH4 + -N and COD. However, keystone species and peripherals that were negatively targeted by their neighbors showed positive correlations with the concentrations of NO2 - -N, polysaccharides, and proteins in the soluble microbial products. The data highlight that the time-series network can provide directional microbial interactions along with the biofilm development process, which would help to predict the tendency of community shifts and propose efficient strategies for the regulation of biofilm-based processes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shasha Yuan
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Sixian Guo
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Xihao Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
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21
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Favila N, Madrigal-Trejo D, Legorreta D, Sánchez-Pérez J, Espinosa-Asuar L, Eguiarte LE, Souza V. MicNet toolbox: Visualizing and unraveling a microbial network. PLoS One 2022; 17:e0259756. [PMID: 35749381 PMCID: PMC9231805 DOI: 10.1371/journal.pone.0259756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 04/05/2022] [Indexed: 11/19/2022] Open
Abstract
Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code's functions with ease.
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Affiliation(s)
- Natalia Favila
- Laboratorio de Inteligencia Artificial, Ixulabs, Mexico City, Mexico
| | - David Madrigal-Trejo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel Legorreta
- Laboratorio de Inteligencia Artificial, Ixulabs, Mexico City, Mexico
| | - Jazmín Sánchez-Pérez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura Espinosa-Asuar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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22
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Krabberød AK, Deutschmann IM, Bjorbækmo MFM, Balagué V, Giner CR, Ferrera I, Garcés E, Massana R, Gasol JM, Logares R. Long-term patterns of an interconnected core marine microbiota. ENVIRONMENTAL MICROBIOME 2022; 17:22. [PMID: 35526063 PMCID: PMC9080219 DOI: 10.1186/s40793-022-00417-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/20/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ocean microbes constitute ~ 70% of the marine biomass, are responsible for ~ 50% of the Earth's primary production and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade. RESULTS Core microbes were defined as those present in > 30% of the monthly samples over 10 years, with the strongest associations. The core microbiota included 259 Operational Taxonomic Units (OTUs) including 182 bacteria, 77 protists, and 1411 strong and mostly positive (~ 95%) associations. Core bacteria tended to be associated with other bacteria, while core protists tended to be associated with bacteria. The richness and abundance of core OTUs varied annually, decreasing in stratified warmers waters and increasing in colder mixed waters. Most core OTUs had a preference for one season, mostly winter, which featured subnetworks with the highest connectivity. Groups of highly associated taxa tended to include protists and bacteria with predominance in the same season, particularly winter. A group of 13 highly-connected hub-OTUs, with potentially important ecological roles dominated in winter and spring. Similarly, 18 connector OTUs with a low degree but high centrality were mostly associated with summer or autumn and may represent transitions between seasonal communities. CONCLUSIONS We found a relatively small and dynamic interconnected core microbiota in a model temperate marine-coastal site, with potential interactions being more deterministic in winter than in other seasons. These core microbes would be essential for the functioning of this ecosystem over the year. Other non-core taxa may also carry out important functions but would be redundant and non-essential. Our work contributes to the understanding of the dynamics and potential interactions of core microbes possibly sustaining ocean ecosystem function.
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Affiliation(s)
- Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway.
| | - Ina M Deutschmann
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Marit F M Bjorbækmo
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway
| | - Vanessa Balagué
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Caterina R Giner
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Isabel Ferrera
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain
| | - Esther Garcés
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
- Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Ramiro Logares
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway.
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
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23
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Shan A, Zhang F, Luan Y. Efficient Approximation of Statistical Significance in Local Trend Analysis of Dependent Time Series. Front Genet 2022; 13:729011. [PMID: 35559007 PMCID: PMC9086404 DOI: 10.3389/fgene.2022.729011] [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: 06/22/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Biological time series data plays an important role in exploring the dynamic changes of biological systems, while the determinate patterns of association between various biological factors can further deepen the understanding of biological system functions and the interactions between them. At present, local trend analysis (LTA) has been commonly conducted in many biological fields, where the biological time series data can be the sequence at either the level of gene expression or OTU abundance, etc., A local trend score can be obtained by taking the similarity degree of the upward, constant or downward trend of time series data as an indicator of the correlation between different biological factors. However, a major limitation facing local trend analysis is that the permutation test conducted to calculate its statistical significance requires a time-consuming process. Therefore, the problem attracting much attention from bioinformatics scientists is to develop a method of evaluating the statistical significance of local trend scores quickly and effectively. In this paper, a new approach is proposed to evaluate the efficient approximation of statistical significance in the local trend analysis of dependent time series, and the effectiveness of the new method is demonstrated through simulation and real data set analysis.
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Affiliation(s)
- Ang Shan
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China
- Postdoctoral Programme of Zhongtai Securities Co. Ltd, Jinan, China
| | - Fang Zhang
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China
| | - Yihui Luan
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China
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24
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Liu Z, Wang J, Meng D, Li L, Liu X, Gu Y, Yan Q, Jiang C, Yin H. The Self-Organization of Marine Microbial Networks under Evolutionary and Ecological Processes: Observations and Modeling. BIOLOGY 2022; 11:biology11040592. [PMID: 35453791 PMCID: PMC9031791 DOI: 10.3390/biology11040592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary The properties and structure of ecological networks in marine microbial communities determine ecosystem functions and stability; however, the principles of microbial network assemblages are poorly understood. In this study, we revealed the influences of species phylogeny and niches on the self-organization of marine microbial co-occurrence networks and provided a mathematical framework to simulate microbial network assemblages. Our results provide deep insights into network stability from the perspective of network assembly principles and not just network properties, such as complexity and modularity. Abstract Evolutionary and ecological processes are primary drivers of ecological network constrictions. However, the ways that these processes underpin self-organization and modularity in networks are poorly understood. Here, we performed network analyses to explore the evolutionary and ecological effects on global marine microbial co-occurrence networks across multiple network levels, including those of nodes, motifs, modules and whole networks. We found that both direct and indirect species interactions were evolutionarily and ecologically constrained across at least four network levels. Compared to ecological processes, evolutionary processes generally showed stronger long-lasting effects on indirect interactions and dominated the network assembly of particle-associated communities in spatially homogeneous environments. Regarding the large network path distance, the contributions of either processes to species interactions generally decrease and almost disappear when network path distance is larger than six. Accordingly, we developed a novel mathematical model based on scale-free networks by considering the joint effects of evolutionary and ecological processes. We simulated the self-organization of microbial co-occurrence networks and found that long-lasting effects increased network stability via decreasing link gain or loss. Overall, these results revealed that evolutionary and ecological processes played key roles in the self-organization and modularization of microbial co-occurrence networks.
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Affiliation(s)
- Zhenghua Liu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China; (Z.L.); (D.M.); (L.L.); (X.L.); (Y.G.)
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China; (Z.L.); (D.M.); (L.L.); (X.L.); (Y.G.)
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China; (Z.L.); (D.M.); (L.L.); (X.L.); (Y.G.)
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China; (Z.L.); (D.M.); (L.L.); (X.L.); (Y.G.)
| | - Yabing Gu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China; (Z.L.); (D.M.); (L.L.); (X.L.); (Y.G.)
| | - Qingyun Yan
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China;
| | - Chengying Jiang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China; (Z.L.); (D.M.); (L.L.); (X.L.); (Y.G.)
- Correspondence:
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25
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Kaiser T, Jahansouz C, Staley C. Network-based approaches for the investigation of microbial community structure and function using metagenomics-based data. Future Microbiol 2022; 17:621-631. [PMID: 35360922 DOI: 10.2217/fmb-2021-0219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Network-based approaches offer a powerful framework to evaluate microbial community organization and function as it relates to a variety of environmental processes. Emerging studies are exploring network theory as a method for data integration that is likely to be critical for the integration of 'omics' data using systems biology approaches. Intricacies of network theory and methodological and computational complexities in network construction, however, impede the use of these tools for translational science. We provide a perspective on the methods of network construction, interpretation and emerging uses for these techniques in understanding host-microbiota interactions.
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Affiliation(s)
- Thomas Kaiser
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA.,Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Cyrus Jahansouz
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher Staley
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA.,Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
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26
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Li H, Luo QP, Pu Q, Yang XR, An XL, Zhu D, Su JQ. Earthworms reduce the dissemination potential of antibiotic resistance genes by changing bacterial co-occurrence patterns in soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:128127. [PMID: 34953254 DOI: 10.1016/j.jhazmat.2021.128127] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Globally distributed earthworms affect compositions of soil compounds, microbial community structures, as well as antibiotic resistance genes (ARGs). Compared to their surroundings, earthworm gut is a simpler environment which could filter out microbes when soil passes through it. However, little is known about how earthworms affect the dissemination of ARGs in soil, and the understanding of the relationship between microbe-microbe interactions and ARGs is still lacking. Here, we designed a microcosm experiment with earthworm addition, and determined bacterial and fungal community compositions based on amplicon sequencing. We also examined mobile genetic elements (MGEs) and ARGs in earthworm gut and soils using high-throughput qPCR. The results showed significant differences of bacterial, fungal and ARG patterns between gut and soil. Earthworms indirectly impacted the patterns of ARGs in soils by affecting bacterial communities and soil properties, which play key roles in the distribution of ARGs and MGEs. The absolute abundances of MGEs in earthworm gut were significantly lower than those in soils, and earthworms reduce the absolute abundance of MGEs in soils. Earthworms changed the microbial co-occurrence patterns, and reduced bacterial connectivity, which were significantly and positively correlated with MGE abundance. These results highlight the importance of earthworm on the distribution and dissemination of ARGs in soils.
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Affiliation(s)
- Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Qiu-Ping Luo
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiang Pu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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27
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Kodera SM, Das P, Gilbert JA, Lutz HL. Conceptual strategies for characterizing interactions in microbial communities. iScience 2022; 25:103775. [PMID: 35146390 PMCID: PMC8819398 DOI: 10.1016/j.isci.2022.103775] [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] [Indexed: 11/17/2022] Open
Abstract
Understanding the sets of inter- and intraspecies interactions in microbial communities is a fundamental goal of microbial ecology. However, the study and quantification of microbial interactions pose several challenges owing to their complexity, dynamic nature, and the sheer number of unique interactions within a typical community. To overcome such challenges, microbial ecologists must rely on various approaches to distill the system of study to a functional and conceptualizable level, allowing for a practical understanding of microbial interactions in both simplified and complex systems. This review broadly addresses the role of several conceptual approaches available for the microbial ecologist’s arsenal, examines specific tools used to accomplish such approaches, and describes how the assumptions, expectations, and philosophies underlying these tools change across scales of complexity.
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Affiliation(s)
- Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Promi Das
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Holly L Lutz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA.,Negaunee Integrative Collections Center, Field Museum of Natural History, Chicago, IL 60605, USA
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28
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Suzuki K, Abe MS, Kumakura D, Nakaoka S, Fujiwara F, Miyamoto H, Nakaguma T, Okada M, Sakurai K, Shimizu S, Iwata H, Masuya H, Nihei N, Ichihashi Y. Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031228. [PMID: 35162258 PMCID: PMC8834966 DOI: 10.3390/ijerph19031228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022]
Abstract
Network-based assessments are important for disentangling complex microbial and microbial–host interactions and can provide the basis for microbial engineering. There is a growing recognition that chemical-mediated interactions are important for the coexistence of microbial species. However, so far, the methods used to infer microbial interactions have been validated with models assuming direct species-species interactions, such as generalized Lotka–Volterra models. Therefore, it is unclear how effective existing approaches are in detecting chemical-mediated interactions. In this paper, we used time series of simulated microbial dynamics to benchmark five major/state-of-the-art methods. We found that only two methods (CCM and LIMITS) were capable of detecting interactions. While LIMITS performed better than CCM, it was less robust to the presence of chemical-mediated interactions, and the presence of trophic competition was essential for the interactions to be detectable. We show that the existence of chemical-mediated interactions among microbial species poses a new challenge to overcome for the development of a network-based understanding of microbiomes and their interactions with hosts and the environment.
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Affiliation(s)
- Kenta Suzuki
- BioResource Research Center, RIKEN, Tsukuba 305-0074, Japan; (H.M.); (Y.I.)
- Correspondence:
| | - Masato S. Abe
- Center for Advanced Intelligence Project, RIKEN, Chuo-ku, Tokyo 103-0027, Japan; (M.S.A.); (S.S.)
| | - Daiki Kumakura
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan; (D.K.); (S.N.)
| | - Shinji Nakaoka
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan; (D.K.); (S.N.)
- Laboratory of Mathematical Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Fuki Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113–8657, Japan; (F.F.); (M.O.); (K.S.); (H.I.)
| | - Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo 271-8501, Japan; (H.M.); (T.N.)
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Sermas Co., Ltd., Ichikawa 272-0015, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University, Matsudo 271-8501, Japan; (H.M.); (T.N.)
- Sermas Co., Ltd., Ichikawa 272-0015, Japan
| | - Mashiro Okada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113–8657, Japan; (F.F.); (M.O.); (K.S.); (H.I.)
| | - Kengo Sakurai
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113–8657, Japan; (F.F.); (M.O.); (K.S.); (H.I.)
| | - Shohei Shimizu
- Center for Advanced Intelligence Project, RIKEN, Chuo-ku, Tokyo 103-0027, Japan; (M.S.A.); (S.S.)
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113–8657, Japan; (F.F.); (M.O.); (K.S.); (H.I.)
| | - Hiroshi Masuya
- BioResource Research Center, RIKEN, Tsukuba 305-0074, Japan; (H.M.); (Y.I.)
| | - Naoto Nihei
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima 960-1296, Japan;
| | - Yasunori Ichihashi
- BioResource Research Center, RIKEN, Tsukuba 305-0074, Japan; (H.M.); (Y.I.)
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29
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Mayerhofer MM, Eigemann F, Lackner C, Hoffmann J, Hellweger FL. Dynamic carbon flux network of a diverse marine microbial community. ISME COMMUNICATIONS 2021; 1:50. [PMID: 37938646 PMCID: PMC9723560 DOI: 10.1038/s43705-021-00055-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 08/19/2021] [Accepted: 09/10/2021] [Indexed: 11/09/2023]
Abstract
The functioning of microbial ecosystems has important consequences from global climate to human health, but quantitative mechanistic understanding remains elusive. The components of microbial ecosystems can now be observed at high resolution, but interactions still have to be inferred e.g., a time-series may show a bloom of bacteria X followed by virus Y suggesting they interact. Existing inference approaches are mostly empirical, like correlation networks, which are not mechanistically constrained and do not provide quantitative mass fluxes, and thus have limited utility. We developed an inference method, where a mechanistic model with hundreds of species and thousands of parameters is calibrated to time series data. The large scale, nonlinearity and feedbacks pose a challenging optimization problem, which is overcome using a novel procedure that mimics natural speciation or diversification e.g., stepwise increase of bacteria species. The method allows for curation using species-level information from e.g., physiological experiments or genome sequences. The product is a mass-balancing, mechanistically-constrained, quantitative representation of the ecosystem. We apply the method to characterize phytoplankton-heterotrophic bacteria interactions via dissolved organic matter in a marine system. The resulting model predicts quantitative fluxes for each interaction and time point (e.g., 0.16 µmolC/L/d of chrysolaminarin to Polaribacter on April 16, 2009). At the system level, the flux network shows a strong correlation between the abundance of bacteria species and their carbon flux during blooms, with copiotrophs being relatively more important than oligotrophs. However, oligotrophs, like SAR11, are unexpectedly high carbon processors for weeks into blooms, due to their higher biomass. The fraction of exudates (vs. grazing/death products) in the DOM pool decreases during blooms, and they are preferentially consumed by oligotrophs. In addition, functional similarity of phytoplankton i.e., what they produce, decouples their association with heterotrophs. The methodology is applicable to other microbial ecosystems, like human microbiome or wastewater treatment plants.
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Affiliation(s)
| | - Falk Eigemann
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
| | - Carsten Lackner
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
| | - Jutta Hoffmann
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
| | - Ferdi L Hellweger
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany.
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30
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Röttjers L, Vandeputte D, Raes J, Faust K. Null-model-based network comparison reveals core associations. ISME COMMUNICATIONS 2021; 1:36. [PMID: 37938641 PMCID: PMC9723671 DOI: 10.1038/s43705-021-00036-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/07/2021] [Accepted: 06/25/2021] [Indexed: 06/15/2023]
Abstract
Microbial network construction and analysis is an important tool in microbial ecology. Such networks are often constructed from statistically inferred associations and may not represent ecological interactions. Hence, microbial association networks are error prone and do not necessarily reflect true community structure. We have developed anuran, a toolbox for investigation of noisy networks with null models. Such models allow researchers to generate data under the null hypothesis that all associations are random, supporting identification of nonrandom patterns in groups of association networks. This toolbox compares multiple networks to identify conserved subsets (core association networks, CANs) and other network properties that are shared across all networks. We apply anuran to a time series of fecal samples from 20 women to demonstrate the existence of CANs in a subset of the sampled individuals. Moreover, we use data from the Global Sponge Project to demonstrate that orders of sponges have a larger CAN than expected at random. In conclusion, this toolbox is a resource for investigators wanting to compare microbial networks across conditions, time series, gradients, or hosts.
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Affiliation(s)
- Lisa Röttjers
- Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Doris Vandeputte
- Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.
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31
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Mikryukov VS, Dulya OV, Likhodeevskii GA, Vorobeichik EL. Analysis of Ecological Networks in Multicomponent Communities of Microorganisms: Possibilities, Limitations, and Potential Errors. RUSS J ECOL+ 2021. [DOI: 10.1134/s1067413621030085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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32
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Matchado MS, Lauber M, Reitmeier S, Kacprowski T, Baumbach J, Haller D, List M. Network analysis methods for studying microbial communities: A mini review. Comput Struct Biotechnol J 2021; 19:2687-2698. [PMID: 34093985 PMCID: PMC8131268 DOI: 10.1016/j.csbj.2021.05.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/01/2021] [Accepted: 05/01/2021] [Indexed: 12/20/2022] Open
Abstract
Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities in complex and contiguous environments. They engage in numerous inter- and intra- kingdom interactions which can be inferred from microbiome profiling data. In particular, network-based approaches have proven helpful in deciphering complex microbial interaction patterns. Here we give an overview of state-of-the-art methods to infer intra-kingdom interactions ranging from simple correlation- to complex conditional dependence-based methods. We highlight common biases encountered in microbial profiles and discuss mitigation strategies employed by different tools and their trade-off with increased computational complexity. Finally, we discuss current limitations that motivate further method development to infer inter-kingdom interactions and to robustly and comprehensively characterize microbial environments in the future.
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Affiliation(s)
- Monica Steffi Matchado
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
| | - Michael Lauber
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
| | - Sandra Reitmeier
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, 85354 Freising, Germany
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, TU Braunschweig and Hannover Medical School, 38106 Brunswick, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), 38106 Brunswick, Germany
| | - Jan Baumbach
- Institute of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
- Chair of Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany
| | - Dirk Haller
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, 85354 Freising, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
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33
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Yang Y, Wang X, Xie K, Zhu C, Chen N, Chen T. kLDM: Inferring Multiple Metagenomic Association Networks based on the Variation of Environmental Factors. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:834-847. [PMID: 33607296 PMCID: PMC9170748 DOI: 10.1016/j.gpb.2020.06.015] [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: 01/08/2019] [Revised: 04/16/2020] [Accepted: 08/15/2020] [Indexed: 11/05/2022]
Abstract
Identification of significant biological relationships or patterns is central to many metagenomic studies. Methods that estimate association networks have been proposed for this purpose; however, they assume that associations are static, neglecting the fact that relationships in a microbial ecosystem may vary with changes in environmental factors (EFs), which can result in inaccurate estimations. Therefore, in this study, we propose a computational model, called the k-Lognormal-Dirichlet-Multinomial (kLDM) model, which estimates multiple association networks that correspond to specific environmental conditions, and simultaneously infers microbe–microbe and EF–microbe associations for each network. The effectiveness of the kLDM model was demonstrated on synthetic data, a colorectal cancer (CRC) dataset, the Tara Oceans dataset, and the American Gut Project dataset. The results revealed that the widely-used Spearman’s rank correlation coefficient method performed much worse than the other methods, indicating the importance of separating samples by environmental conditions. Cancer fecal samples were then compared with cancer-free samples, and the estimation achieved by kLDM exhibited fewer associations among microbes but stronger associations between specific bacteria, especially five CRC-associated operational taxonomic units, indicating gut microbe translocation in cancer patients. Some EF-dependent associations were then found within a marine eukaryotic community. Finally, the gut microbial heterogeneity of inflammatory bowel disease patients was detected. These results demonstrate that kLDM can elucidate the complex associations within microbial ecosystems. The kLDM program, R, and Python scripts, together with all experimental datasets, are accessible at https://github.com/tinglab/kLDM.git.
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Affiliation(s)
- Yuqing Yang
- Department of Computer Science and Technology and Institute of Artificial Intelligence, Tsinghua University, Beijing 100084, China; Sogou Inc., Beijing 100084, China
| | - Xin Wang
- Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100005, China; Department of Ultrasound, Peking Union Medical College Hospital, Beijing 100005, China
| | - Kaikun Xie
- Department of Computer Science and Technology and Institute of Artificial Intelligence, Tsinghua University, Beijing 100084, China
| | - Congmin Zhu
- Department of Computer Science and Technology and Institute of Artificial Intelligence, Tsinghua University, Beijing 100084, China; Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Ning Chen
- Department of Computer Science and Technology and Institute of Artificial Intelligence, Tsinghua University, Beijing 100084, China.
| | - Ting Chen
- Department of Computer Science and Technology and Institute of Artificial Intelligence, Tsinghua University, Beijing 100084, China; Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; Beijing National Research Center for Information Science and Technology, Beijing 100084, China.
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The sum is greater than the parts: exploiting microbial communities to achieve complex functions. Curr Opin Biotechnol 2021; 67:149-157. [PMID: 33561703 DOI: 10.1016/j.copbio.2021.01.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Multi-species microbial communities are ubiquitous in nature. The widespread prevalence of these communities is due to highly elaborated interactions among their members thereby accomplishing metabolic functions that are unattainable by individual members alone. Harnessing these communal capabilities is an emerging field in biotechnology. The rational intervention of microbial communities for the purpose of improved function has been facilitated in part by developments in multi-omics approaches, synthetic biology, and computational methods. Recent studies have demonstrated the benefits of rational interventions to human and animal health as well as agricultural productivity. Emergent technologies, such as in situ modification of complex microbial community and community metabolic modeling, represent an avenue to engineer sustainable microbial communities. In this opinion, we review relevant computational and experimental approaches to study and engineer microbial communities and discuss their potential for biotechnological applications.
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Liang Z, Xu G, Shi J, Yu S, Lu Q, Liang D, Sun L, Wang S. Sludge digestibility and functionally active microorganisms in methanogenic sludge digesters revealed by E. coli-fed digestion and microbial source tracking. ENVIRONMENTAL RESEARCH 2021; 193:110539. [PMID: 33253703 DOI: 10.1016/j.envres.2020.110539] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/19/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Methanogenic sludge digestion plays a pivotal role in attenuating and hygienizing the massively-produced waste activated sludge (WAS), which is predominantly composed of microbial cells and extracellular polymeric substances (EPS). The efficient sludge digestion requires a variety of functionally active microorganisms working together closely to convert sludge organic matter into biogas. Nonetheless, the digestion efficiency (or digestibility quantified as carbon removal efficiency) of major sludge constituents (i.e., microbial cells and EPS) and associated functionally active microorganisms in sludge digesters remain elusive. In this study, we identified the digestibility of sludge microbial cells and the associated functionally active microorganisms by using Escherichia coli (E. coli)-fed digestion and microbial source tracking. The average carbon removals in four digesters fed with fresh WAS (WAS-AD), thermal pretreated WAS (Thermal-WAS-AD), E. coli cells (E.coli-AD) and thermal pretreated E. coli cells (Thermal-E.coli-AD) were 30.6 ± 3.4%, 45.8 ± 2.9%, 69.0 ± 3.4% and 68.9 ± 4.6%, respectively. Compared to WAS-AD and Thermal-WAS-AD, the significantly higher carbon removals in E. coli-AD and Thermal-E. coli-AD suggested the remarkably higher digestibility of microbial cells than EPS, and releasing organic matter from EPS might be a rate-limiting step in sludge digestion. Functionally active microorganisms for microbial cell digestion predominantly included fermenters (e.g., Petrimonas and Lentimicrobium), syntrophic acetogens (e.g., Synergistaceae) and methanogens (e.g., Methanosaeta and Methanosarcina). Microbial source tracking estimation showed that the microbial cell-digesting populations accounted for 35.6 ± 9.1% and 70.3 ± 10.1% of total microbial communities in the WAS-AD and Thermal-WAS-AD, respectively. Accordingly, the functionally active microorganisms for digestion of both microbial cells and EPS accounted for 64.5 ± 12.1% and 97.3 ± 2.0% of total digestion sludge microbiome in WAS-AD and Thermal-WAS-AD, respectively. By contrast, feeding WAS-derived microorganisms accounted for 23.2 ± 4.4% and 2.3 ± 1.2% of total microbial communities in the WAS-AD and Thermal-WAS-AD, respectively.
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Affiliation(s)
- Zhiwei Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Guofang Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jiangjian Shi
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Sining Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qihong Lu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Dawei Liang
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Space & Environment, Beihang University, Beijing, 100191, China
| | - Lianpeng Sun
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275, China.
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Zhao X, Yang Y, Feng K, Wang X, Liu B, Xie G, Xing D. Self-regulating microbiome networks ensure functional resilience of biofilms in sand biofilters during manganese load fluctuations. WATER RESEARCH 2021; 188:116473. [PMID: 33038718 DOI: 10.1016/j.watres.2020.116473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/20/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
Sand biofilters (SBFs) are commonly used to remove manganese (Mn(II)) from drinking water. Mn(II) load variation frequently occurs in SBFs due to fluctuating influent Mn(II) concentrations or flow rates. Therefore, it is important to understand the responses of microbial biofilms in SBFs to environmental disturbances and how they affect Mn(II) oxidation efficiency. Here, the responses of microbial ecological networks and Mn(II) removal in SBFs to increasing Mn(II) load were investigated. The Mn(II) removal efficiency in two SBFs remained at 99.8% despite an increase in influent Mn(II) from 2 mg/L to 4 mg/L, but significantly deteriorated (50.1-58.5%) upon increasing the filtration rate. A canonical correlation analysis of the microbial communities indicated that the local Mn(II) concentration and biofilter depth impacted community compositions of biofilms. The dominant species within the biofilms exhibited clear stratification, with simple associations in the upper layer of the SBFs and more complex interspecies interactions in the bottom layers. Putative manganese-oxidizing bacteria Hyphomicrobium and Pedomicrobium dominated the microbiomes in different layers of SBFs, and changed relatively little in abundance when Mn(II) and filtration rate increased. The community networks showed that biofilm microbiomes in SBFs were resilient to the disturbance of Mn(II) load, primarily via regulating microbial interactions. High manganese loads negatively affected the functional modules for Mn(II) removal. Furthermore, the relatively rare species Candidatus Entotheonella palauensis was identified as a module hub, implying taxa with low abundances can have important roles in ecosystem function. These results shed new light on the ecological rules guiding responses of microbiomes in sand biofilters to environmental stress.
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Affiliation(s)
- Xin Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, P.O. Box 2614, 73 Huanghe Road, Nangang District, Harbin, Heilongjiang Province 150090, China
| | - Yang Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, P.O. Box 2614, 73 Huanghe Road, Nangang District, Harbin, Heilongjiang Province 150090, China
| | - Kun Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, P.O. Box 2614, 73 Huanghe Road, Nangang District, Harbin, Heilongjiang Province 150090, China
| | - Xiuheng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, P.O. Box 2614, 73 Huanghe Road, Nangang District, Harbin, Heilongjiang Province 150090, China
| | - Bingfeng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, P.O. Box 2614, 73 Huanghe Road, Nangang District, Harbin, Heilongjiang Province 150090, China
| | - Guojun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, P.O. Box 2614, 73 Huanghe Road, Nangang District, Harbin, Heilongjiang Province 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, P.O. Box 2614, 73 Huanghe Road, Nangang District, Harbin, Heilongjiang Province 150090, China.
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Cyriaque V, Géron A, Billon G, Nesme J, Werner J, Gillan DC, Sørensen SJ, Wattiez R. Metal-induced bacterial interactions promote diversity in river-sediment microbiomes. FEMS Microbiol Ecol 2020; 96:5826176. [PMID: 32343356 DOI: 10.1093/femsec/fiaa076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023] Open
Abstract
Anthropogenic metal contamination results in long-term environmental selective pressure with unclear impacts on bacterial communities, which comprise key players in ecosystem functioning. Since metal contamination poses serious toxicity and bioaccumulation issues, assessing their impact on environmental microbiomes is important to respond to current environmental and health issues. Despite elevated metal concentrations, the river sedimentary microbiome near the MetalEurop foundry (France) shows unexpected higher diversity compared with the upstream control site. In this work, a follow-up of the microbial community assembly during a metal contamination event was performed in microcosms with periodic renewal of the supernatant river water. Sediments of the control site were gradually exposed to a mixture of metals (Cd, Cu, Pb and Zn) in order to reach similar concentrations to MetalEurop sediments. Illumina sequencing of 16S rRNA gene amplicons was performed. Metal-resistant genes, czcA and pbrA, as well as IncP plasmid content, were assessed by quantitative PCR. The outcomes of this study support previous in situ observations showing that metals act as community assembly managers, increasing diversity. This work revealed progressive adaptation of the sediment microbiome through the selection of different metal-resistant mechanisms and cross-species interactions involving public good-providing bacteria co-occurring with the rest of the community.
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Affiliation(s)
- Valentine Cyriaque
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Augustin Géron
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium.,Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling,FK9 4LA, UK
| | - Gabriel Billon
- Univ. Lille, CNRS, UMR 8516 - LASIRE - LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, F-59000 Lille, France
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, D-18119 Rostock, Germany
| | - David C Gillan
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
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Transformation of Microbial Negative Correlations into Positive Correlations by Saccharomyces cerevisiae Inoculation during Pomegranate Wine Fermentation. Appl Environ Microbiol 2020; 86:AEM.01847-20. [PMID: 33036987 DOI: 10.1128/aem.01847-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/01/2020] [Indexed: 11/20/2022] Open
Abstract
The application of starter is a common practice to accelerate and steer the pomegranate wine fermentation process. However, the use of starter needs a better understanding of the effect of the interaction between the starter and native microorganisms during alcoholic fermentation. In this study, high-throughput sequencing combined with metabolite analysis was applied to analyze the effect of commercial Saccharomyces cerevisiae inoculation on the native fungal community interaction and metabolism during pomegranate wine fermentation. Results showed that there were diverse native fungi in pomegranate juice, including Hanseniaspora uvarum, Hanseniaspora valbyensis, S. cerevisiae, Pichia terricola, and Candida diversa Based on ecological network analysis, we found that S. cerevisiae inoculation transformed the negative correlations into positive correlations among the native fungal communities and decreased the Granger causalities between native yeasts and volatile organic compounds. This might lead to decreased contents of isobutanol, isoamylol, octanoic acid, decanoic acid, ethyl laurate, ethyl acetate, ethyl hexadecanoate, phenethyl acetate, and 2-phenylethanol during fermentation. This study combined correlation and causality analysis to gain a more integrated understanding of microbial interaction and the fermentation process. It provided a new strategy to predict certain behaviors between inoculated and selected microorganisms and those coming directly from the fruit.IMPORTANCE Microbial interactions play an important role in flavor metabolism during traditional food and beverage fermentation. However, we understand little about how selected starters influence interactions among native microorganisms. In this study, we found that S. cerevisiae inoculation changed the interactions and metabolisms of native fungal communities during pomegranate wine fermentation. This study not only suggests that starter inoculation should take into account the positive features of starters but also characterizes the microbial interactions established among the starters and the native communities. It may be helpful to select appropriate starter cultures for winemakers to design different styles of wine.
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Fournier B, Pereira Dos Santos S, Gustavsen JA, Imfeld G, Lamy F, Mitchell EAD, Mota M, Noll D, Planchamp C, Heger TJ. Impact of a synthetic fungicide (fosetyl-Al and propamocarb-hydrochloride) and a biopesticide (Clonostachys rosea) on soil bacterial, fungal, and protist communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:139635. [PMID: 32534282 DOI: 10.1016/j.scitotenv.2020.139635] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 05/27/2023]
Abstract
The use of synthetic pesticides in agriculture is increasingly debated. However, few studies have compared the impact of synthetic pesticides and alternative biopesticides on non-target soil microorganisms playing a central role in soil functioning. We conducted a mesocosm experiment and used high-throughput amplicon sequencing to test the impact of a fungal biopesticide and a synthetic fungicide on the diversity, the taxonomic and functional compositions, and co-occurrence patterns of soil bacterial, fungal and protist communities. Neither the synthetic pesticide nor the biopesticide had a significant effect on microbial α-diversity. However, both types of pesticides decreased the complexity of the soil microbial network. The two pesticides had contrasting impacts on the composition of microbial communities and the identity of key taxa as revealed by microbial network analyses. The biopesticide impacted keystone taxa that structured the soil microbial network. The synthetic pesticide modified biotic interactions favouring taxa that are less efficient at degrading organic compounds. This suggests that the biopesticides and the synthetic pesticide have different impact on soil functioning. Altogether, our study shows that pest management products may have functionally significant impacts on the soil microbiome even if microbial α-diversity is unaffected. It also illustrates the potential of high-throughput sequencing analyses to improve the ecotoxicological risk assessment of pesticides on non-target soil microorganisms.
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Affiliation(s)
- Bertrand Fournier
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland; Institute of Environmental Science and Geography, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Sofia Pereira Dos Santos
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland.
| | | | - Gwenaël Imfeld
- Université de Strasbourg, Laboratory of Hydrology and Geochemistry of Strasbourg (LHyGeS), UMR 7517 CNRS/EOST, 1 Rue Blessig, 67084 Strasbourg Cedex, France.
| | - Frédéric Lamy
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland.
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile Argand 11, 2000 Neuchâtel, Switzerland; Jardin Botanique de Neuchâtel, Chemin du Pertuis-du-Sault 58, 2000 Neuchâtel, Switzerland.
| | - Matteo Mota
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland.
| | - Dorothea Noll
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland.
| | - Chantal Planchamp
- Soil and Biotechnology Division, Federal Office for the Environment (FOEN), 3003 Bern, Switzerland.
| | - Thierry J Heger
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland.
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Regularized S-Map Reveals Varying Bacterial Interactions. Appl Environ Microbiol 2020; 86:AEM.01615-20. [PMID: 32801185 DOI: 10.1128/aem.01615-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
There is a growing awareness that bacterial interactions follow a highly nonlinear pattern in reality. However, it is challenging to track the varying bacterial interactions using pairwise correlation analysis, which fails to explore their potential effects on the behavior of microbes. Here, we utilized a regularized sequential locally weighted global linear map (S-map) to capture the varying interspecific interactions from the time series data of a bacterial community under exposure to nitrite. Our results show that bacterial interactions are highly variable and that asymmetric interactions dominate the interaction pattern in a community. Furthermore, we propose a Jacobian coefficient-based statistical method to predict the harmony level of a bacterial community at each successive ecosystem state. The results show that the bacterial community exhibits a higher harmony level in nitrite-treated samples than in the control group. We show that the community harmony level is positively associated with the specific endogenous respiration rates and biofilm formation of the culture. In addition, the community tends to process lower diversity and structural stability under zero- and high-nitrite stresses. We demonstrate that the harmony level, rather than structural stability, is a useful index for unveiling the underlying mechanism of bacterial performance. Overall, the regularized S-map can help us to understand bacterial interactions in ecosystems more accurately than previous approaches.IMPORTANCE It has long been acknowledged that bacterial interactions play important roles in community structure and function. Revealing the interaction variability can allow an understanding of how bacteria respond to perturbation and why bacterial community performance changes. Such information should improve our skills in engineering bacterial communities (e.g., in a wastewater treatment plant) and achieve better removal performance and lower energy consumption.
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Liu Y, Blain S, Crispi O, Rembauville M, Obernosterer I. Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler. Environ Microbiol 2020; 22:3968-3984. [PMID: 32755055 DOI: 10.1111/1462-2920.15184] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/10/2020] [Accepted: 08/01/2020] [Indexed: 11/29/2022]
Abstract
The Southern Ocean remains one of the least explored marine environments. The investigation of temporal microbial dynamics has thus far been hampered by the limited access to this remote ocean. We present here high-resolution seasonal observations of the prokaryotic community composition during phytoplankton blooms induced by natural iron fertilization. A total of 18 seawater samples were collected by a moored remote autonomous sampler over 4 months at 5-11 day intervals in offshore surface waters (central Kerguelen Plateau). Illumina sequencing of the 16S rRNA gene revealed that among the most abundant amplicon sequence variants, SAR92 and Aurantivirga were the first bloom responders, Pseudomonadaceae, Nitrincolaceae and Polaribacter had successive peaks during the spring bloom decline, and Amylibacter increased in relative abundance later in the season. SAR11 and SUP05 were abundant prior to and after the blooms. Using network analysis, we identified two groups of diatoms representative of the spring and summer bloom that had opposite correlation patterns with prokaryotic taxa. Our study provides the first seasonal picture of microbial community dynamics in the open Southern Ocean and thereby offers biological insights to the cycling of carbon and iron, and to an important puzzling issue that is the modest nitrate decrease associated to iron fertilization.
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Affiliation(s)
- Yan Liu
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France.,College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Life Sciences, Ludong University, Yantai, China
| | - Stéphane Blain
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Olivier Crispi
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Mathieu Rembauville
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Ingrid Obernosterer
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
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Shao Q, Lin Z, Zhou C, Yan X. Bacterioplankton assembly and interspecies interactions follow trajectories of Gymnodinium-diatom bloom. MARINE ENVIRONMENTAL RESEARCH 2020; 160:105010. [PMID: 32907730 DOI: 10.1016/j.marenvres.2020.105010] [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: 12/02/2019] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
The underlying mechanisms of bacterioplankton community assembly and interspecies interactions during harmful algal blooms remain largely unclear. Using 16S rRNA gene amplicon sequencing, we analyzed the bacterioplankton communities over the continuous course of saxitoxin-producing Gymnodinium catenatum blooms and two diatom (i.e., Skeletonema costatum and Chaetoceros curvisetus) blooms in an anthropogenically controlled and eutrophic bay, East China Sea. The succession of bacterioplankton communities correlated with changes in the dynamics of algal species. Deterministic versus stochastic bacterioplankton community assemblage processes were quantified, demonstrating that stochastic processes increased when algal blooms happened. The occurrence of algal blooms caused weaker bacterioplankton interspecies interactions and higher degrees of cooperative activities, changed keystone taxa and diminished the stability of bacterial communities. These findings consequently have important implications for our understanding of bacterioplankton community ecology during algal blooms.
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Affiliation(s)
- Qianwen Shao
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China; Ningbo Institute of Oceanography, Ningbo 315832, China
| | - Zhongzhou Lin
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China; Ningbo Institute of Oceanography, Ningbo 315832, China
| | - Chengxu Zhou
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China.
| | - Xiaojun Yan
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China.
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Xia P, Yan D, Sun R, Song X, Lin T, Yi Y. Community composition and correlations between bacteria and algae within epiphytic biofilms on submerged macrophytes in a plateau lake, southwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138398. [PMID: 32335447 DOI: 10.1016/j.scitotenv.2020.138398] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
Epiphytic biofilms are complex matrix-enclosed communities comprising large numbers of bacteria and algae, which play an important role in the biogeochemical cycles in aquatic systems. However, little is known about the correlations that occur between these communities or the relative impact of environmental factors on their composition. In this study, epiphytic biofilms on three different aquatic plants were sampled in a typical plateau lake (Caohai, southwest China) in July and November of 2018. Bacterial diversity was assessed using Miseq sequencing approaches and algal communities were assessed using light microscopy. Gammaproteobacteria (54.64%), Bacteroidetes (17.50%) and Firmicutes (13.99%) were the dominant bacterial taxa and Chlorophyta (47.62%), Bacillariophyta (28.57%) and Euglenophyta (19.05%) were the dominant algae. The alpha diversity values of the epiphytic bacterial and algal communities were greater during the macrophyte decline period (November) than during the growth period (July). Microbial community composition was significantly affected by abiotic factors (water temperature, NH4+, pH or TP) and biotic factors (algae or bacteria). Interestingly, in July and November, the epiphytic algal community dissimilarity was stronger than that observed for bacterial community dissimilarity, suggesting that bacterial community dissimilarity may increase more slowly with environmental change than algal community dissimilarity. Furthermore, association network analysis revealed complex correlations between algal biomass and bacteria phylotype, and that 67.83% of correlations were positive and 32.17% were negative. This may indicate that facilitative correlations between algae and bacteria are predominant in epiphytic biofilms. These results provide new information on algal-bacterial correlations as well as the possible mechanisms that drive variations in the microbial community in epiphytic biofilms in freshwater lakes.
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Affiliation(s)
- Pinhua Xia
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China
| | - Dingbo Yan
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China
| | - Rongguo Sun
- College of Chemistry and Material, Guizhou Normal University, Guiyang, PR China
| | - Xu Song
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China
| | - Tao Lin
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China
| | - Yin Yi
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China; The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry and Grassland Administration, Guizhou Normal University, Guiyang, 550001, PR China.
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Zhang L, Zhao F, Li X, Lu W. Contribution of influent rivers affected by different types of pollution to the changes of benthic microbial community structure in a large lake. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 198:110657. [PMID: 32344267 DOI: 10.1016/j.ecoenv.2020.110657] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/01/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
As a microbial group in watershed ecosystems, the bacterial community is a sensitive indicator of external environmental fluctuations. However, the effects of different sources of exogenous pollution on the diversity and structure of bacterial communities in inflow rivers and lakes have not been studied in depth. In this study, we used 16S rRNA gene sequencing technology to study the diversity and composition of bacterial communities in rivers affected by different types of pollution. The results showed that the composition of the bacterial communities in rivers with different exogenous pollution sources was different. For example, the genus Arenimonas, which belongs to the Gamma-proteobacteria, is extensively enriched in IDPR (industrially and domestically polluted rivers) and ADPR (agriculturally and domestically polluted rivers) (KW, p < 0.05), while the genus Micromonospora is a more unique genus found in APR (agriculturally polluted rivers). When exploring the topology and classification characteristics of river microbial symbiosis models, it was found that the bacterial community symbiosis network is divided into six modules under different exogenous pollution regimes, and the nodes in the different modules perform different functions, such as the IDPR-dominated module I. In the network, the relatively abundant the genus Flavobacterium and the genus Nitrospira are the key factors driving the nitrogen cycle in the watershed where the samples were collected. In addition, our research indicates that communities in lake environments may be more susceptible to disturbances of various physiological or functional redundancies, thus retaining their original community structure. Overall, this study emphasizes that adaptive changes in the bacterial community structure of the sediments in the catchment and the occurrence of interactions are responses to different exogenous pollution sources.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China.
| | - Feng Zhao
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Xingchen Li
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Wenxuan Lu
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
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Xu L, Zhang B, Peng X, Zhang X, Sun B, Sun H, Jiang C, Zhou S, Zeng X, Bai Z, Xu S, Zhuang X. Dynamic variations of microbial community structure in Myriophyllum aquaticum constructed wetlands in response to different NH4+-N concentrations. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.02.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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46
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Xia Y. Correlation and association analyses in microbiome study integrating multiomics in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:309-491. [PMID: 32475527 DOI: 10.1016/bs.pmbts.2020.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.
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Affiliation(s)
- Yinglin Xia
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
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47
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Eetemadi A, Rai N, Pereira BMP, Kim M, Schmitz H, Tagkopoulos I. The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health. Front Microbiol 2020; 11:393. [PMID: 32318028 PMCID: PMC7146706 DOI: 10.3389/fmicb.2020.00393] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/26/2020] [Indexed: 12/12/2022] Open
Abstract
Food and human health are inextricably linked. As such, revolutionary impacts on health have been derived from advances in the production and distribution of food relating to food safety and fortification with micronutrients. During the past two decades, it has become apparent that the human microbiome has the potential to modulate health, including in ways that may be related to diet and the composition of specific foods. Despite the excitement and potential surrounding this area, the complexity of the gut microbiome, the chemical composition of food, and their interplay in situ remains a daunting task to fully understand. However, recent advances in high-throughput sequencing, metabolomics profiling, compositional analysis of food, and the emergence of electronic health records provide new sources of data that can contribute to addressing this challenge. Computational science will play an essential role in this effort as it will provide the foundation to integrate these data layers and derive insights capable of revealing and understanding the complex interactions between diet, gut microbiome, and health. Here, we review the current knowledge on diet-health-gut microbiota, relevant data sources, bioinformatics tools, machine learning capabilities, as well as the intellectual property and legislative regulatory landscape. We provide guidance on employing machine learning and data analytics, identify gaps in current methods, and describe new scenarios to be unlocked in the next few years in the context of current knowledge.
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Affiliation(s)
- Ameen Eetemadi
- Department of Computer Science, University of California, Davis, Davis, CA, United States
- Genome Center, University of California, Davis, Davis, CA, United States
| | - Navneet Rai
- Genome Center, University of California, Davis, Davis, CA, United States
| | - Beatriz Merchel Piovesan Pereira
- Genome Center, University of California, Davis, Davis, CA, United States
- Department of Microbiology, University of California, Davis, Davis, CA, United States
| | - Minseung Kim
- Department of Computer Science, University of California, Davis, Davis, CA, United States
- Genome Center, University of California, Davis, Davis, CA, United States
- Process Integration and Predictive Analytics (PIPA LLC), Davis, CA, United States
| | - Harold Schmitz
- Graduate School of Management, University of California, Davis, Davis, CA, United States
| | - Ilias Tagkopoulos
- Department of Computer Science, University of California, Davis, Davis, CA, United States
- Genome Center, University of California, Davis, Davis, CA, United States
- Process Integration and Predictive Analytics (PIPA LLC), Davis, CA, United States
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48
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Qin N, Liang P, Wu C, Wang G, Xu Q, Xiong X, Wang T, Zolfo M, Segata N, Qin H, Knight R, Gilbert JA, Zhu TF. Longitudinal survey of microbiome associated with particulate matter in a megacity. Genome Biol 2020; 21:55. [PMID: 32127018 PMCID: PMC7055069 DOI: 10.1186/s13059-020-01964-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/18/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND While the physical and chemical properties of airborne particulate matter (PM) have been extensively studied, their associated microbiome remains largely unexplored. Here, we performed a longitudinal metagenomic survey of 106 samples of airborne PM2.5 and PM10 in Beijing over a period of 6 months in 2012 and 2013, including those from several historically severe smog events. RESULTS We observed that the microbiome composition and functional potential were conserved between PM2.5 and PM10, although considerable temporal variations existed. Among the airborne microorganisms, Propionibacterium acnes, Escherichia coli, Acinetobacter lwoffii, Lactobacillus amylovorus, and Lactobacillus reuteri dominated, along with several viral species. We further identified an extensive repertoire of genes involved in antibiotic resistance and detoxification, including transporters, transpeptidases, and thioredoxins. Sample stratification based on Air Quality Index (AQI) demonstrated that many microbial species, including those associated with human, dog, and mouse feces, exhibit AQI-dependent incidence dynamics. The phylogenetic and functional diversity of air microbiome is comparable to those of soil and water environments, as its composition likely derives from a wide variety of sources. CONCLUSIONS Airborne particulate matter accommodates rich and dynamic microbial communities, including a range of microbial elements that are associated with potential health consequences.
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Affiliation(s)
- Nan Qin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China. .,Realbio Genomics Institute, Shanghai, 200050, China.
| | - Peng Liang
- School of Life Sciences, Peking University, Beijing, 100871, China.,School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Chunyan Wu
- Realbio Genomics Institute, Shanghai, 200050, China
| | - Guanqun Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Qian Xu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.,Realbio Genomics Institute, Shanghai, 200050, China
| | - Xiao Xiong
- Realbio Genomics Institute, Shanghai, 200050, China
| | | | - Moreno Zolfo
- Centre for Integrative Biology, University of Trento, 38123, Trento, Italy
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, 38123, Trento, Italy
| | - Huanlong Qin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. .,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China.
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49
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Whelan FJ, Rusilowicz M, McInerney JO. Coinfinder: detecting significant associations and dissociations in pangenomes. Microb Genom 2020; 6:e000338. [PMID: 32100706 PMCID: PMC7200068 DOI: 10.1099/mgen.0.000338] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/23/2020] [Indexed: 12/16/2022] Open
Abstract
The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are 'coincident') more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3 and R and is freely available under the GNU license from https://github.com/fwhelan/coinfinder.
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Affiliation(s)
- Fiona Jane Whelan
- School of Life Sciences, The University of Nottingham, Nottingham, UK
| | - Martin Rusilowicz
- Faculty of Biology, Medicine & Health, The University of Manchester, Manchester, UK
| | - James Oscar McInerney
- School of Life Sciences, The University of Nottingham, Nottingham, UK
- Faculty of Biology, Medicine & Health, The University of Manchester, Manchester, UK
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50
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Dam P, Rodriguez-R LM, Luo C, Hatt J, Tsementzi D, Konstantinidis KT, Voit EO. Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes. Sci Rep 2020; 10:2423. [PMID: 32051429 PMCID: PMC7016141 DOI: 10.1038/s41598-020-58769-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 01/15/2020] [Indexed: 11/09/2022] Open
Abstract
Lake Lanier (Georgia, USA) is home to more than 11,000 microbial Operational Taxonomic Units (OTUs), many of which exhibit clear annual abundance patterns. To assess the dynamics of this microbial community, we collected time series data of 16S and 18S rRNA gene sequences, recovered from 29 planktonic shotgun metagenomic datasets. Based on these data, we constructed a dynamic mathematical model of bacterial interactions in the lake and used it to analyze changes in the abundances of OTUs. The model accounts for interactions among 14 sub-communities (SCs), which are composed of OTUs blooming at the same time of the year, and three environmental factors. It captures the seasonal variations in abundances of the SCs quite well. Simulation results suggest that changes in water temperature affect the various SCs differentially and that the timing of perturbations is critical. We compared the model results with published results from Lake Mendota (Wisconsin, USA). These comparative analyses between lakes in two very different geographical locations revealed substantially more cooperation and less competition among species in the warmer Lake Lanier than in Lake Mendota.
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Affiliation(s)
- Phuongan Dam
- Department of Biomedical Engineering, Georgia Tech, Atlanta, GA, USA
| | - Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA
| | - Chengwei Luo
- School of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA
| | - Janet Hatt
- School of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA
| | | | - Eberhard O Voit
- Department of Biomedical Engineering, Georgia Tech, Atlanta, GA, USA.
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