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Yang J, Liu W, Han X, Hao X, Yao Q, Du W. Gut microbiota modulation enhances the immune capacity of lizards under climate warming. MICROBIOME 2024; 12:37. [PMID: 38388458 PMCID: PMC10882899 DOI: 10.1186/s40168-023-01736-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/04/2023] [Indexed: 02/24/2024]
Abstract
BACKGROUND Host-microbial interactions are expected to affect species' adaptability to climate change but have rarely been explored in ectothermic animals. Some studies have shown that short-term warming reduced gut microbial diversity that could hamper host functional performance. RESULTS However, our longitudinal experiments in semi-natural conditions demonstrated that warming decreased gut microbiota diversity at 2 months, but increased diversity at 13 and 27 months in a desert lizard (Eremias multiocellata). Simultaneously, long-term warming significantly increased the antibacterial activity of serum, immune responses (higher expression of intestinal immune-related genes), and the concentration of short-chain fatty acids (thereby intestinal barrier and immunity) in the lizard. Fecal microbiota transplant experiments further revealed that increased diversity of gut microbiota significantly enhanced antibacterial activity and the immune response of lizards. More specifically, the enhanced immunity is likely due to the higher relative abundance of Bacteroides in warming lizards, given that the bacteria of Bacteroides fragilis regulated IFN-β expression to increase the immune response of lizards under a warming climate. CONCLUSIONS Our study suggests that gut microbiota can help ectotherms cope with climate warming by enhancing host immune response, and highlights the importance of long-term studies on host-microbial interactions and their biological impacts.
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Affiliation(s)
- Jing Yang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiqiang Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingzhi Han
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
| | - Xin Hao
- School of Tropical Agriculture and Forestry (School of Agricultural and Rural, School of Rural Revitalization), Hainan University, Danzhou, 571737, China
| | - Qibin Yao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiguo Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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Xu A, Liu C, Zhao S, Song Z, Sun H. Dynamic distribution of Massilia spp. in sewage, substrate, plant rhizosphere/phyllosphere and air of constructed wetland ecosystem. Front Microbiol 2023; 14:1211649. [PMID: 37577432 PMCID: PMC10413979 DOI: 10.3389/fmicb.2023.1211649] [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: 04/25/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Massilia bacteria are widely distributed and have various ecological functions. Preliminary studies have shown that Massilia is the dominant species in constructed wetland ecosystems, but its species composition and distribution in constructed wetlands are still unclear. Methods In this paper, the in-house-designed primers were used to construct a 16S rDNA clone library of Massilia. The RFLP sequence analysis method was used to analyze the diversity of Massilia clone library and the composition of Massilia in sewage, substrate, plant rhizosphere, plant phyllosphere and air in a constructed wetland sewage treatment system. Redundancy analysis (RDA) and canonical correspondence analysis (CCA) were used to analyze the correlation between environmental factors and the population characteristics of Massilia in the corresponding environment. The dominant species of Massilia were analyzed for differences. Results The results showed that the 16S rDNA clone library in primer 5 worked well. According to the clone library diversity index analysis, the richness of Massilia varied significantly in different environments in different seasons, where the overall summer and autumn richness was higher than that in the spring and winter. The relative abundance of 5 Massilia in the constructed wetland ecosystem was greater than 1% in all samples, which were M. alkalitolerans, M. albidiflava, M. aurea, M. brevitalea, and M. timonae. The seasonal variation of dominant genera was significantly correlated with environmental factors in constructed wetlands. Discussion The above results indicated that the species of Massilia were abundant and widely distributed in the constructed wetland ecosystem, and there were significant seasonal differences. In addition, the Massilia clone library of constructed wetland was constructed for the first time in this study and the valuable data of Massilia community structure were provided, which was conducive to the further study of microbial community in constructed wetland.
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Affiliation(s)
- Ailing Xu
- School of Environmental and Municipal Engineering, Qingdao Technological University, Qingdao, Shandong, China
| | - Congcong Liu
- School of Environmental and Municipal Engineering, Qingdao Technological University, Qingdao, Shandong, China
| | - Shuke Zhao
- Qingdao sub-Center, Shandong Water Transfer Project Operation and Maintenance Center, Qingdao, Shandong, China
| | - Zhiwen Song
- School of Environmental and Municipal Engineering, Qingdao Technological University, Qingdao, Shandong, China
| | - Hui Sun
- Qingdao sub-Center, Shandong Water Transfer Project Operation and Maintenance Center, Qingdao, Shandong, China
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Xu M, Huang XH, Gao P, Chen HQ, Yuan Q, Zhu YX, Shen XX, Zhang YY, Xue ZX. Insight into the spatiotemporal distribution of antibiotic resistance genes in estuarine sediments during long-term ecological restoration. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 335:117472. [PMID: 36827800 DOI: 10.1016/j.jenvman.2023.117472] [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: 10/08/2022] [Revised: 01/16/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
In this study, we aimed to investigate the long-term spatiotemporal changes in hydrodynamics, antibiotics, nine typical subtypes of antibiotic resistance genes (ARGs), class 1 integron gene (intI1), and microbial communities in the sediments of a semi-enclosed estuary during ecological restoration with four treatment stages (influent (#1), effluent of the biological treatment area (#2), oxic area (#3), and plant treatment area (#4)). Ecological restoration of the estuary reduced common pollutants (nitrogen and phosphorus) in the water, whereas variations in ARGs showed noticeable seasonal and spatial features. The absolute abundance of ARGs at sampling site #2 considerably increased in autumn and winter, while it significantly increased at sampling site #3 in spring and summer. The strong intervention of biological treatment (from #1 to #2) and aerators (from #2 to #3) in the estuary substantially affected the distribution of ARGs and dominant antibiotic-resistant bacteria (ARB). The dominant ARB (Thiobacillus) in estuarine sediments may have low abundance but important dissemination roles. Meanwhile, redundancy and network analysis revealed that the microbial communities and intl1 were key factors related to ARG dissemination, which was affected by spatial and seasonal ecological restoration. A positive correlation between low flow velocity and certain ARGs (tetM, tetW, tetA, sul2, and ermC) was observed, implying that flow optimization should also be considered in future ecological restoration to remediate ARGs. Furthermore, the absolute abundance of ARGs can be utilized as an index to evaluate the removal capacity of ARGs by estuarine restoration.
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Affiliation(s)
- Ming Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Xing-Hao Huang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Peng Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Hao-Qiang Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Quan Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Yun-Xiang Zhu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Xiao-Xiao Shen
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.
| | - Yan-Yan Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Zhao-Xia Xue
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China.
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Hoque MN, Rahman MS, Islam T, Sultana M, Crandall KA, Hossain MA. Induction of mastitis by cow-to-mouse fecal and milk microbiota transplantation causes microbiome dysbiosis and genomic functional perturbation in mice. Anim Microbiome 2022; 4:43. [PMID: 35794639 PMCID: PMC9258091 DOI: 10.1186/s42523-022-00193-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mastitis pathogenesis involves a wide range of opportunistic and apparently resident microorganims including bacteria, viruses and archaea. In dairy animals, microbes reside in the host, interact with environment and evade the host immune system, providing a potential for host-tropism to favor mastitis pathogenesis. To understand the host-tropism phenomena of bovine-tropic mastitis microbiomes, we developed a cow-to-mouse mastitis model. METHODS A cow-to-mouse mastitis model was established by fecal microbiota transplantation (FMT) and milk microbiota transplantation (MMT) to pregnant mice to assess microbiome dysbiosis and genomic functional perturbations through shotgun whole metagenome sequencing (WMS) along with histopathological changes in mice mammary gland and colon tissues. RESULTS The cow-to-mouse FMT and MMT from clinical mastitis (CM) cows induced mastitis syndromes in mice as evidenced by histopathological changes in mammary gland and colon tissues. The WMS of 24 samples including six milk (CM = 3, healthy; H = 3), six fecal (CM = 4, H = 2) samples from cows, and six fecal (CM = 4, H = 2) and six mammary tissue (CM = 3, H = 3) samples from mice generating 517.14 million reads (average: 21.55 million reads/sample) mapped to 2191 bacterial, 94 viral and 54 archaeal genomes. The Kruskal-Wallis test revealed significant differences (p = 0.009) in diversity, composition, and relative abundances in microbiomes between CM- and H-metagenomes. These differences in microbiome composition were mostly represented by Pseudomonas aeruginosa, Lactobacillus crispatus, Klebsiella oxytoca, Enterococcus faecalis, Pantoea dispersa in CM-cows (feces and milk), and Muribaculum spp., Duncaniella spp., Muribaculum intestinale, Bifidobacterium animalis, Escherichia coli, Staphylococcus aureus, Massilia oculi, Ralstonia pickettii in CM-mice (feces and mammary tissues). Different species of Clostridia, Bacteroida, Actinobacteria, Flavobacteriia and Betaproteobacteria had a strong co-occurrence and positive correlation as the indicator species of murine mastitis. However, both CM cows and mice shared few mastitis-associated microbial taxa (1.14%) and functional pathways regardless of conservation of mastitis syndromes, indicating the higher discrepancy in mastitis-associated microbiomes among lactating mammals. CONCLUSIONS We successfully induced mastitis by FMT and MMT that resulted in microbiome dysbiosis and genomic functional perturbations in mice. This study induced mastitis in a mouse model through FMT and MMT, which might be useful for further studies- focused on pathogen(s) involved in mastitis, their cross-talk among themselves and the host.
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Affiliation(s)
- M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, 1706, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
- Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
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Santibáñez R, Lara F, Barros TM, Mardones E, Cuadra F, Thomson P. Ocular Microbiome in a Group of Clinically Healthy Horses. Animals (Basel) 2022; 12:ani12080943. [PMID: 35454190 PMCID: PMC9028004 DOI: 10.3390/ani12080943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/22/2022] [Accepted: 03/31/2022] [Indexed: 02/01/2023] Open
Abstract
The ocular microbiome in horses is poorly described compared to other species, and most of the information available in the literature is based on traditional techniques, which has limited the depth of the knowledge on the subject. The objective of this study was to characterize and predict the metabolic pathways of the ocular microbiome of a group of healthy horses. Conjunctival swabs were obtained from both eyes of 14 horses, and DNA extraction was performed from the swabs, followed by next generation sequencing and bioinformatics analyses employing DADA2 and PICRUSt2. A total of 17 phyla were identified, of which Pseudomonadota (Proteobacteria) was the most abundant (59.88%), followed by Actinomycetota (Actinobacteria) (22.44%) and Bacteroidota (Bacteroidetes) (16.39%), totaling an average of 98.72% of the communities. Similarly, of the 278 genera identified, Massilia, Pedobacter, Pseudomonas, Sphingomonas, Suttonella and Verticia were present in more than 5% of the samples analyzed. Both Actinobacteria and Bacteroides showed great heterogeneity within the samples. The most abundant inferred metabolic functions were related to vital functions for bacteria such as aerobic respiration, amino acid, and lipid biosynthesis.
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Affiliation(s)
- Rodrigo Santibáñez
- Departamento de Ingeniería Química y Bioprocesos, Facultad de Ingeniería, Pontificia Universidad Católica, Santiago 8940000, Chile;
| | - Felipe Lara
- Unidad de Cirugía y Medicina Equina, Hospital Clínico Veterinario, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370134, Chile;
| | - Teresa M. Barros
- Department of Clinical Science, College of Veterinary Medicine Specialty Ophthalmology Intern, Vaughan Large Animal Teaching Hospital, Auburn, AL 36832, USA;
| | - Elizabeth Mardones
- Laboratorio de Microbiología Clínica y Microbioma, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370134, Chile; (E.M.); (F.C.)
| | - Françoise Cuadra
- Laboratorio de Microbiología Clínica y Microbioma, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370134, Chile; (E.M.); (F.C.)
| | - Pamela Thomson
- Laboratorio de Microbiología Clínica y Microbioma, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370134, Chile; (E.M.); (F.C.)
- Correspondence: ; Tel.: +56-227-703-688
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Holochová P, Mašlaňová I, Sedláček I, Švec P, Králová S, Kovařovic V, Busse HJ, Staňková E, Barták M, Pantůček R. Description of Massilia rubra sp. nov., Massilia aquatica sp. nov., Massilia mucilaginosa sp. nov., Massilia frigida sp. nov., and one Massilia genomospecies isolated from Antarctic streams, lakes and regoliths. Syst Appl Microbiol 2020; 43:126112. [PMID: 32847787 DOI: 10.1016/j.syapm.2020.126112] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 11/24/2022]
Abstract
Bacteria of the genus Massilia often colonize extreme ecosystems, however, a detailed study of the massilias from the Antarctic environment has not yet been performed. Here, sixty-four Gram-stain-negative, aerobic, motile rods isolated from different environmental samples on James Ross Island (Antarctica) were subjected to a polyphasic taxonomic study. The psychrophilic isolates exhibited slowly growing, moderately slimy colonies revealing bold pink-red pigmentation on R2A agar. The set of strains exhibited the highest 16S rRNA gene sequence similarities (99.5-99.9%) to Massilia violaceinigra B2T and Massilia atriviolacea SODT and formed several phylogenetic groups based on the analysis of gyrB and lepA genes. Phenotypic characteristics allowed four of them to be distinguished from each other and from their closest relatives. Compared to the nearest phylogenetic neighbours the set of six genome-sequenced representatives exhibited considerable phylogenetic distance at the whole-genome level. Bioinformatic analysis of the genomic sequences revealed a high number of putative genes involved in oxidative stress response, heavy-metal resistance, bacteriocin production, the presence of putative genes involved in nitrogen metabolism and auxin biosynthesis. The identification of putative genes encoding aromatic dioxygenases suggests the biotechnology potential of the strains. Based on these results four novel species and one genomospecies of the genus Massilia are described and named Massilia rubra sp. nov. (P3094T=CCM 8692T=LMG 31213T), Massilia aquatica sp. nov. (P3165T=CCM 8693T=LMG 31211T), Massilia mucilaginosa sp. nov. (P5902T=CCM 8733T=LMG 31210T), and Massilia frigida sp. nov. (P5534T=CCM 8695T=LMG 31212T).
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Affiliation(s)
- Pavla Holochová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Ivana Mašlaňová
- Department of Experimental Biology, Section of Genetics and Molecular Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Vojtěch Kovařovic
- Department of Experimental Biology, Section of Genetics and Molecular Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Miloš Barták
- Department of Experimental Biology, Section of Experimental Plant Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Roman Pantůček
- Department of Experimental Biology, Section of Genetics and Molecular Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic.
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