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Lanzoni O, Szokoli F, Schrallhammer M, Sabaneyeva E, Krenek S, Doak TG, Verni F, Berendonk TU, Castelli M, Petroni G. "Candidatus Intestinibacterium parameciiphilum"-member of the "Candidatus Paracaedibacteraceae" family (Alphaproteobacteria, Holosporales) inhabiting the ciliated protist Paramecium. Int Microbiol 2024; 27:659-671. [PMID: 37615902 PMCID: PMC11144129 DOI: 10.1007/s10123-023-00414-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023]
Abstract
Protists frequently host diverse bacterial symbionts, in particular those affiliated with the order Holosporales (Alphaproteobacteria). All characterised members of this bacterial lineage have been retrieved in obligate association with a wide range of eukaryotes, especially multiple protist lineages (e.g. amoebozoans, ciliates, cercozoans, euglenids, and nucleariids), as well as some metazoans (especially arthropods and related ecdysozoans). While the genus Paramecium and other ciliates have been deeply investigated for the presence of symbionts, known members of the family "Candidatus Paracaedibacteraceae" (Holosporales) are currently underrepresented in such hosts. Herein, we report the description of "Candidatus Intestinibacterium parameciiphilum" within the family "Candidatus Paracaedibacteraceae", inhabiting the cytoplasm of Paramecium biaurelia. This novel bacterium is almost twice as big as its relative "Candidatus Intestinibacterium nucleariae" from the opisthokont Nuclearia and does not present a surrounding halo. Based on phylogenetic analyses of 16S rRNA gene sequences, we identified six further potential species-level lineages within the genus. Based on the provenance of the respective samples, we investigated the environmental distribution of the representatives of "Candidatus Intestinibacterium" species. Obtained results are consistent with an obligate endosymbiotic lifestyle, with protists, in particular freshwater ones, as hosts. Thus, available data suggest that association with freshwater protists could be the ancestral condition for the members of the "Candidatus Intestinibacterium" genus.
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Affiliation(s)
| | - Franziska Szokoli
- Department of Biology, University of Pisa, Pisa, Italy
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Martina Schrallhammer
- Mikrobiologie, Institut für Biologie II, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Elena Sabaneyeva
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Sascha Krenek
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | | | - Franco Verni
- Department of Biology, University of Pisa, Pisa, Italy
| | - Thomas U Berendonk
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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Bombaywala S, Bajaj A, Dafale NA. Meta-analysis of wastewater microbiome for antibiotic resistance profiling. J Microbiol Methods 2024; 223:106953. [PMID: 38754482 DOI: 10.1016/j.mimet.2024.106953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/12/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
The microbial composition and stress molecules are main drivers influencing the development and spread of antibiotic resistance bacteria (ARBs) and genes (ARGs) in the environment. A reliable and rapid method for identifying associations between microbiome composition and resistome remains challenging. In the present study, secondary metagenome data of sewage and hospital wastewaters were assessed for differential taxonomic and ARG profiling. Subsequently, Random Forest (RF)-based ML models were used to predict ARG profiles based on taxonomic composition and model validation on hospital wastewaters. Total ARG abundance was significantly higher in hospital wastewaters (15 ppm) than sewage (5 ppm), while the resistance towards methicillin, carbapenem, and fluoroquinolone were predominant. Although, Pseudomonas constituted major fraction, Streptomyces, Enterobacter, and Klebsiella were characteristic of hospital wastewaters. Prediction modeling showed that the relative abundance of pathogenic genera Escherichia, Vibrio, and Pseudomonas contributed most towards variations in total ARG count. Moreover, the model was able to identify host-specific patterns for contributing taxa and related ARGs with >90% accuracy in predicting the ARG subtype abundance. More than >80% accuracy was obtained for hospital wastewaters, demonstrating that the model can be validly extrapolated to different types of wastewater systems. Findings from the study showed that the ML approach could identify ARG profile based on bacterial composition including 16S rDNA amplicon data, and can serve as a viable alternative to metagenomic binning for identification of potential hosts of ARGs. Overall, this study demonstrates the promising application of ML techniques for predicting the spread of ARGs and provides guidance for early warning of ARBs emergence.
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Affiliation(s)
- Sakina Bombaywala
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Abhay Bajaj
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nishant A Dafale
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Zhang S, Liu S, Liu H, Li H, Luo J, Zhang A, Ding Y, Ren T, Chen W. Stochastic Assembly Increases the Complexity and Stability of Shrimp Gut Microbiota During Aquaculture Progression. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:92-102. [PMID: 38165637 DOI: 10.1007/s10126-023-10279-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
The gut microbiota of aquaculture species contributes to their food metabolism and regulates their health, which has been shown to vary during aquaculture progression of their hosts. However, limited research has examined the outcomes and mechanisms of these changes in the gut microbiota of hosts. Here, Kuruma shrimps from the beginning, middle, and late stages of aquaculture progression (about a time duration of 2 months between each stage) were collected and variations in the gut microbiota of Kuruma shrimp during the whole aquaculture process were examined. High-throughput sequencing demonstrated increases in the diversity and richness of the shrimp gut microbiota with aquaculture progression. In addition, the gut microbiota composition differed among cultural stages, with enrichment of Firmicutes, RF39, and Megamonas and a reduction in Proteobacteria in the mid-stage. Notably, only very few taxa were persistent in the shrimp gut microbiota during the whole aquaculture progression, while the number of taxa that specific to the end of aquaculture was high. Network analysis revealed increasing complexity of the shrimp gut microbiota during aquaculture progression. Moreover, the shrimp gut microbiota became significantly more stable towards the end of aquaculture. According to the results of neutral community model, contribution of stochastic processes for shaping the shrimp gut microbiota was elevated along the aquaculture progression. This study showed substantial variations in shrimp gut microbiota during aquaculture progression and explored the underlying mechanisms regulating these changes.
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Affiliation(s)
- Saisai Zhang
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Shuang Liu
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Hongwei Liu
- Dalian Ocean University, Dalian Liaoning, 116023, China
| | - Hui Li
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Jun Luo
- Dalian Sun Asia Tourism Holding Co. Ltd., Dalian, Liaoning, 116023, China
| | - Aili Zhang
- Dalian Ocean School, Dalian, Liaoning, 116023, China
| | - Yinpeng Ding
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Tongjun Ren
- Dalian Ocean University, Dalian Liaoning, 116023, China
| | - Wenbo Chen
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China.
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Guan X, Zhao Z, Jiang J, Fu L, Liu J, Pan Y, Gao S, Wang B, Chen Z, Wang X, Sun H, Jiang B, Dong Y, Zhou Z. Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:545-556. [PMID: 37537784 PMCID: PMC10667648 DOI: 10.1111/1758-2229.13188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.
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Affiliation(s)
- Xiaoyan Guan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Zelong Zhao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Jingwei Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Lei Fu
- Dalian Salt Chemical Group Co., LtdDalianLiaoningPeople's Republic of China
| | - Jiaojiao Liu
- Dalian Salt Chemical Group Co., LtdDalianLiaoningPeople's Republic of China
| | - Yongjia Pan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Shan Gao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Bai Wang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Zhong Chen
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Xuda Wang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Hongjuan Sun
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Bing Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Ying Dong
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Zunchun Zhou
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
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Yu J, Jiang C, Yamano R, Koike S, Sakai Y, Mino S, Sawabe T. Unveiling the early life core microbiome of the sea cucumber Apostichopus japonicus and the unexpected abundance of the growth-promoting Sulfitobacter. Anim Microbiome 2023; 5:54. [PMID: 37876012 PMCID: PMC10599069 DOI: 10.1186/s42523-023-00276-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Microbiome in early life has long-term effects on the host's immunological and physiological development and its disturbance is known to trigger various diseases in host Deuterostome animals. The sea cucumber Apostichopus japonicus is one of the most valuable marine Deuterostome invertebrates in Asia and a model animal in regeneration studies. To understand factors that impact on host development and holobiont maintenance, host-microbiome association has been actively studied in the last decade. However, we currently lack knowledge of early life core microbiome during its ontogenesis and how it benefits the host's growth. RESULTS We analyzed the microbial community in 28 sea cucumber samples from a laboratory breeding system, designed to replicate aquaculture environments, across six developmental stages (fertilized eggs to the juvenile stage) over a three years-period to examine the microbiomes' dynamics and stability. Microbiome shifts occurred during sea cucumber larval ontogenesis in every case. Application of the most sophisticated core microbiome extraction methodology, a hybrid approach with abundance-occupancy core microbiome analyses (top 75% of total reads and > 70% occupation) and core index calculation, first revealed early life core microbiome consisted of Alteromonadaceae and Rhodobacteraceae, as well as a stage core microbiome consisting of pioneer core microbe Pseudoalteromonadaceae in A. japonicus, suggesting a stepwise establishment of microbiome related to ontogenesis and feeding behavior in A. japonicus. More interestingly, four ASVs affiliated to Alteromonadaceae and Rhodobacteraceae were extracted as early life core microbiome. One of the ASV (ASV0007) was affiliated to the Sulfitobactor strain BL28 (Rhodobacteraceae), isolated from blastula larvae in the 2019 raring batch. Unexpectedly, a bioassay revealed the BL28 strain retains a host growth-promoting ability. Further meta-pangenomics approach revealed the BL28 genome reads were abundant in the metagenomic sequence pool, in particular, in that of post-gut development in early life stages of A. japonicus. CONCLUSION Repeated rearing efforts of A. japonicus using laboratory aquaculture replicating aquaculture environments and hybrid core microbiome extraction approach first revealed particular ASVs affiliated to Alteromonadaceae and Rhodobacteraceae as the A. japonicus early life core microbiome. Further bioassay revealed the growth promoting ability to the host sea cucumber in one of the core microbes, the Sulfitobactor strain BL28 identified as ASV0007. Genome reads of the BL28 were abundant in post-gut development of A. japonicus, which makes us consider effective probiotic uses of those core microbiome for sea cucumber resource production and conservation. The study also emphasizes the importance of the core microbiome in influencing early life stages in marine invertebrates. Understanding these dynamics could offer pathways to improve growth, immunity, and disease resistance in marine invertebrates.
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Affiliation(s)
- Juanwen Yu
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
| | - Chunqi Jiang
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Ryota Yamano
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Shotaro Koike
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Yuichi Sakai
- Hakodate Fisheries Research, Hokkaido Research Organization, Local Independent Administrative Agency, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
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Wang X, Zhao Z, Jiang J, Mi R, Guan X, Dong Y, Li S, Chen Z, Gao S, Wang B, Xiao Y, Pan Y, Zhou Z. Temporal stability and assembly mechanisms of gut microbiota in sea cucumbers response to nanoplastics treatment. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115407. [PMID: 37639828 DOI: 10.1016/j.ecoenv.2023.115407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/13/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Aquaculture provides essential food for humans, and the health of farmed species is particularly important for the aquaculture industry. Aquaculture environment could be a sink of plastic debris (PDs) due to the enclosed character and heavy use of plastics. Gut microbiota of aquaculture species could respond to the exogenous pollutants and regulate the health of hosts. Here, variations in gut microbiota of Apostichopus japonicus induced by the ingested nanoplastics (NPs) were investigated by a lab experiment. We selected a NPs concentration gradient of 100 mg/kg and 500 mg/kg to simulate microplastic pollution to A. japonicus, and the significant differences in gut microbiota composition after 21 days of NP exposure were evaluated. According to the high-throughput sequencing from time series samples, a decrease of diversity in gut microbiota of A. japonicus with dietary NPs was observed. In addition, the gut microbiota compositions of sea cucumbers with and without NPs exposure were also distinct, expressing as enrichment of Bacteroidota while reducement of Proteobacteria under NPs stresses. Combined the results of network analysis, the less complexity and stability of gut microbiota in sea cucumbers with dietary NPs were proved. Based on the neutral community model, the ingested NPs elevated the contribution of stochastic processes for the gut microbiota assembly in sea cucumbers. Our study showed that substantial variations in gut microbiota of A. japonicus under NPs stresses, and also explored the underlying mechanisms regulating these changes. This research would offer new meaningful insights into the toxicity of NPs on sea cucumbers, contributing a solid fundament to improve the health of sea cucumbers under NPs stresses.
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Affiliation(s)
- Xuda Wang
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zelong Zhao
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Jingwei Jiang
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Rui Mi
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xiaoyan Guan
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Ying Dong
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shilei Li
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zhong Chen
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shan Gao
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bai Wang
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Yao Xiao
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Yongjia Pan
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
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Liu HQ, Zhao ZL, Li HJ, Yu SJ, Cong L, Ding LL, Ran C, Wang XF. Accurate prediction of huanglongbing occurrence in citrus plants by machine learning-based analysis of symbiotic bacteria. FRONTIERS IN PLANT SCIENCE 2023; 14:1129508. [PMID: 37313258 PMCID: PMC10258322 DOI: 10.3389/fpls.2023.1129508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/02/2023] [Indexed: 06/15/2023]
Abstract
Huanglongbing (HLB), the most prevalent citrus disease worldwide, is responsible for substantial yield and economic losses. Phytobiomes, which have critical effects on plant health, are associated with HLB outcomes. The development of a refined model for predicting HLB outbreaks based on phytobiome markers may facilitate early disease detection, thus enabling growers to minimize damages. Although some investigations have focused on differences in the phytobiomes of HLB-infected citrus plants and healthy ones, individual studies are inappropriate for generating common biomarkers useful for detecting HLB on a global scale. In this study, we therefore obtained bacterial information from several independent datasets representing hundreds of citrus samples from six continents and used these data to construct HLB prediction models based on 10 machine learning algorithms. We detected clear differences in the phyllosphere and rhizosphere microbiomes of HLB-infected and healthy citrus samples. Moreover, phytobiome alpha diversity indices were consistently higher for healthy samples. Furthermore, the contribution of stochastic processes to citrus rhizosphere and phyllosphere microbiome assemblies decreased in response to HLB. Comparison of all constructed models indicated that a random forest model based on 28 bacterial genera in the rhizosphere and a bagging model based on 17 bacterial species in the phyllosphere predicted the health status of citrus plants with almost 100% accuracy. Our results thus demonstrate that machine learning models and phytobiome biomarkers may be applied to evaluate the health status of citrus plants.
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Affiliation(s)
- Hao-Qiang Liu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Ze-long Zhao
- Shanghai BIOZERON Biotechnology Co., Ltd., Shanghai, China
| | - Hong-Jun Li
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Shi-Jiang Yu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Lin Cong
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Li-Li Ding
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Chun Ran
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Xue-Feng Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
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8
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Zhang Z, Ding M, Sun Y, Khattak RH, Chen J, Teng L, Liu Z. Different living environments drive deterministic microbial community assemblages in the gut of Alpine musk deer ( Moschus chrysogaster). Front Microbiol 2023; 13:1108405. [PMID: 36713154 PMCID: PMC9880224 DOI: 10.3389/fmicb.2022.1108405] [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: 11/26/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Substantial variation in the environment directly causes remodeling of the colonized gut microbiota, controlling community diversity, and functions in the host to tune-up their adaptive states. However, the mechanisms of microbial community assembly in response to environmental changes remain unclear, especially in endangered ruminants. In this study, we analyzed the microbial communities of 37 fecal samples collected from captive and wild Alpine musk deer (Moschus chrysogaster) to characterize the complexity and assembly processes using 16S rRNA gene sequencing. We found significantly different diversities and compositions of gut microbiota among both groups associated with different living environments. Heterogeneous selection was the predominant factor regulating the gut microbiota community under similar climatic conditions, indicating that microbial community assembly was largely driven by deterministic mechanisms. The species co-occurrence network showed complex and tight connections with a higher positive correlation in the wild environment. Moreover, the captive group exhibited significant differences in chemoheterotrophy and fermentation compared with the wild group, but the opposite was observed in animal parasites or symbionts, which might be closely related to diet, energy supply, and healthcare of animals. This study provides a framework basis and new insights into understanding gut microbiota in different environments.
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Affiliation(s)
- Zhirong Zhang
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China
| | - Mengqi Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Yujiao Sun
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China,College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Romaan Hayat Khattak
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China
| | - Junda Chen
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China
| | - Liwei Teng
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China,Key Laboratory of Conservation Biology, National Forestry and Grassland Administration, Harbin, China,*Correspondence: Liwei Teng ✉
| | - Zhensheng Liu
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China,Key Laboratory of Conservation Biology, National Forestry and Grassland Administration, Harbin, China,Zhensheng Liu ✉
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Zhou L, Zhao Z, Shao L, Fang S, Li T, Gan L, Guo C. Predicting the abundance of metal resistance genes in subtropical estuaries using amplicon sequencing and machine learning. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113844. [PMID: 36068766 DOI: 10.1016/j.ecoenv.2022.113844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/24/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Heavy metals are a group of anthropogenic contaminants in estuary ecosystems. Bacteria in estuaries counteract the highly concentrated metal toxicity through metal resistance genes (MRGs). Presently, metagenomic technology is popularly used to study MRGs. However, an easier and less expensive method of acquiring MRG information is needed to deepen our understanding of the fate of MRGs. Thus, this study explores the feasibility of using a machine learning approach-namely, random forests (RF)-to predict MRG abundance based on the 16S rRNA amplicon sequenced datasets from subtropical estuaries in China. Our results showed that the total MRG abundance could be predicted by RF models using bacterial composition at different taxonomic levels. Among them, the relative abundance of bacterial phyla had the highest predicted accuracy (71.7 %). In addition, the RF models constructed by bacterial phyla predicted the abundance of six MRG types and nine MRG subtypes with substantial accuracy (R2 > 0.600). Five bacterial phyla (Firmicutes, Bacteroidetes, Patescibacteria, Armatimonadetes, and Nitrospirae) substantially determined the variations in MRG abundance. Our findings prove that RF models can predict MRG abundance in South China estuaries during the wet season by using the bacterial composition obtained by 16S rRNA amplicon sequencing.
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Affiliation(s)
- Lei Zhou
- College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Liyi Shao
- College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Shiyun Fang
- College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Tongzhou Li
- College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Lihong Gan
- College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Chuanbo Guo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Xu L, Xiang P, Zhang B, Yang K, Liu F, Wang Z, Jin Y, Deng L, Gan W, Song Z. Host Species Influence the Gut Microbiota of Endemic Cold-Water Fish in Upper Yangtze River. Front Microbiol 2022; 13:906299. [PMID: 35923412 PMCID: PMC9339683 DOI: 10.3389/fmicb.2022.906299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
The fish gut microbiome plays an important role in nutrition absorption and energy metabolism. Studying the gut microbes of cold-water fish is important to understand the dietary adaptation strategies in extreme environments. In this study, the gut samples of Schizothorax wangchiachii (SW, herbivorous), Schizothorax kozlovi (SK, omnivorous), and Percocypris pingi (PP, carnivorous) in the upper Yangtze River were collected, and we sequenced 16S rRNA amplicon to study the potential relationship between gut microbes and host species. The results showed that gut microbial composition and diversity were significantly different between the three cold-water fishes. These fishes had different key taxa in their gut microbes, including bacteria involved in the breakdown of food (e.g., Cetobacterium, Aeromonas, and Clostridium sensu stricto 10). The highest alpha diversity indices (e.g., Chao 1 index) were identified in the herbivore (SW), followed by the carnivore (PP), and the lowest in the omnivore (SK). Non-metric multidimensional scaling (NMDS) results revealed that the gut microbial community of these species was different between host species. The neutral community model (NCM) showed that the microbial community structure of SW was shaped by stochastic processes, and the highest species dispersal was found in SW, followed by PP, and the lowest in SK. The results of niche breadth agreed with these findings. Our results demonstrated that host species influenced the gut microbiome composition, diversity, and microbial community assembly processes of the three cold-water fishes. These findings implied that the variation of gut microbiome composition and function plays a key role in digesting and absorbing nutrients from different foods in cold-water fish.
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Affiliation(s)
- Liangliang Xu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Peng Xiang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Baowen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kun Yang
- Institute of Ecology, China West Normal University, Nanchong, China
| | - Fenglin Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zesong Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yanjun Jin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Longjun Deng
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Weixiong Gan
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Zhaobin Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Zhaobin Song,
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