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Wang W, Zhang S, Gao T, Li L. In-situ treatment of gaseous benzene in fixed-bed biofilter with polyurethane foam: Functional population response and benzene transformation pathway. BIORESOURCE TECHNOLOGY 2024; 405:130926. [PMID: 38824970 DOI: 10.1016/j.biortech.2024.130926] [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: 05/14/2024] [Accepted: 05/31/2024] [Indexed: 06/04/2024]
Abstract
Volatile organic compounds emitted from landfills posed adverse effect on health. In this study, gaseous benzene was biologically treated using an in-situ biofilter without air pump. Its performance was investigated and the removal efficiency of benzene reached over 90 %. The decrease in the average benzene concentration was consistent with first-order reaction kinetics. Mycolicibacterium dominated the bacterial consortium (41-57 %) throughout the degradation. Annotation of genes by metagenomic analysis helped to deduce the degradation pathways (benzene degradation, catechol ortho-cleavage and meta-cleavage) and to reveal the contribution of different species to the degradation process. In total, 21 kinds of key genes and 13 enzymes were involved in the three modules of benzene transformation. Mycolicibacter icosiumassiliensis and Sphingobium sp. SCG-1 carried multiple functional genes critically involved in benzene biodegradation. These findings provide technical and theoretical support for the in-situ bioremediation of benzene-contaminated soil and waste gas reduction in landfills.
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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, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyan Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Tong Gao
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco- Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco- Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
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Hou J, Hull V, Fujimoto M, Zhang Z, Chen X, Chen S, Chen R, Connor T, Qi D, Zhang J. Characterizing the metabolome and microbiome at giant panda scent marking sites during the mating season. iScience 2024; 27:110051. [PMID: 38904067 PMCID: PMC11186968 DOI: 10.1016/j.isci.2024.110051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/02/2024] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
Scent marking sites served as a primary means of chemical communication for giant pandas, enabling intraspecific communication. We integrated metabolomics and high-throughput sequencing techniques to examine the non-targeted metabolome and microbial community structure of scent marking sites and feces in the field. Integrative analysis revealed a more comprehensive array of chemical compounds compared to previous investigations, including ketones, acids, heterocycles, alcohols, and aldehydes. Notably, specific compounds such as 2-decenal, (E)-, octanal, decanal, L-α-terpineol, vanillin, and nonanal emerged as potential key players in scent signaling. Intriguingly, our study of the microbial domain identified dominant bacterial species from the Actinobacteria, Bacteroidetes, and Proteobacteria phyla, likely orchestrating metabolic processes at scent marking sites. Comparative analyses showed, for the first time, that feces do not share the same functions as scent markers, indicating distinct functional roles. This research deepens scientific understanding of chemical communication in wild pandas.
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Affiliation(s)
- Jin Hou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan Province 637002, China
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Vanessa Hull
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, USA
| | - Masanori Fujimoto
- Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Zejun Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan Province 637002, China
| | - Xiaoyuan Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan Province 637002, China
| | - Shiyu Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan Province 637002, China
| | - Rui Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan Province 637002, China
| | - Thomas Connor
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province 610081, China
| | - Jindong Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan Province 637002, China
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3
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Hu Y, Hu Y, Zhou W, Wei F. Conservation Genomics and Metagenomics of Giant and Red Pandas in the Wild. Annu Rev Anim Biosci 2024; 12:69-89. [PMID: 37863091 DOI: 10.1146/annurev-animal-021022-054730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Giant pandas and red pandas are endangered species with similar specialized bamboo diet and partial sympatric distribution in China. Over the last two decades, the rapid development of genomics and metagenomics research on these species has enriched our knowledge of their biology, ecology, physiology, genetics, and evolution, which is crucial and useful for their conservation. We describe the evolutionary history, endangerment processes, genetic diversity, and population structure of wild giant pandas and two species of red pandas (Chinese and Himalayan red pandas). In addition, we explore how genomics and metagenomics studies have provided insight into the convergent adaptation of pandas to the specialized bamboo diet. Finally, we discuss how these findings are applied to effective conservation management of giant and red pandas in the wild and in captivity to promote the long-term persistence of these species.
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Affiliation(s)
- Yisi Hu
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fuwen Wei
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Wei J, Zheng Z, Hou X, Jia F, Yuan Y, Yuan F, He F, Hu L, Zhao L. Echinacoside inhibits colorectal cancer metastasis via modulating the gut microbiota and suppressing the PI3K/AKT signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:116866. [PMID: 37429503 DOI: 10.1016/j.jep.2023.116866] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/10/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Echinacoside (ECH) is the dominant phenylethanoid glycoside-structured compound identified from our developed herbal formula Huangci granule, which has been previously reported to inhibit the invasion and metastasis of CRC and prolong patients' disease-free survival duration. Though ECH has inhibitory activity against aggressive colorectal cancer (CRC) cells, its anti-metastasis effect in vivo and the action mechanism is undetermined. Given that ECH has an extremely low bioavailability and gut microbiota drives the CRC progression, we hypothesized that ECH could inhibit metastatic CRC by targeting the gut microbiome. AIM OF THE STUDY The purpose of this study was to investigate the impact of ECH on colorectal cancer liver metastasis in vivo and its potential mechanisms. MATERIALS AND METHODS An intrasplenic injection-induced liver metastatic model was established to examine the efficiency of ECH on tumor metastasis in vivo. Fecal microbiota from the model group and the ECH group were separately transplanted into pseudo-sterile CRLM mice in order to verify the role of gut flora in the ECH anti-metastatic effect. The 16S rRNA gene sequence was applied to analyze the structure and composition of the gut microbiota after ECH intervention, and the effect of ECH on short-chain fatty acid (SCFAs)-producing bacteria growth was proven by anaerobic culturing in vitro. GC-MS was applied to quantitatively analyze the serum SCFAs levels in mice. RNA-seq was performed to detect the gene changes involving tumor-promoting signaling pathway. RESULTS ECH inhibited CRC metastasis in a dose-dependent manner in the metastatic colorectal cancer (mCRC) mouse model. Manipulation of gut bacteria in the mCRC mouse model further proved that SCFA-generating gut bacteria played an indispensable role in mediating the antimetastatic action of ECH. Under an anaerobic condition, ECH benefited SCFA-producing microbiota without affecting the total bacterial load, presenting a dose-dependent promotion on the growth of a butyrate producer, Faecalibacterium prausnitzii (F.p). Furthermore, ECH-reshaped or F.p-colonized microbiota with a high butyrate-producing capability inhibited liver metastasis by suppressing PI3K/AKT signaling and reversing the epithelial-mesenchymal transition (EMT) process, whereas this anti-metastatic ability was abrogated by the butyrate synthase inhibitor heptanoyl-CoA. CONCLUSION This study demonstrated that ECH exhibits oral anti-metastatic efficacy by facilitating butyrate-producing gut bacteria, which downregulates PI3K/AKT signaling and EMT. It hints at a novel role for ECH in CRC therapy.
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Affiliation(s)
- Jiao Wei
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zongmei Zheng
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xinxin Hou
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fengjing Jia
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuan Yuan
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fuwen Yuan
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Feng He
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Liang Hu
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Ling Zhao
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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Rojas CA, Marks SL, Borras E, Lesea H, McCartney MM, Coil DA, Davis CE, Eisen JA. Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics. Sci Rep 2023; 13:19382. [PMID: 37938241 PMCID: PMC10632438 DOI: 10.1038/s41598-023-45997-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Many mammals rely on volatile organic chemical compounds (VOCs) produced by bacteria for their communication and behavior, though little is known about the exact molecular mechanisms or bacterial species that are responsible. We used metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium, Bacteroides, Proteus, Lactobacillus, and Streptococcus, and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r = 0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of importance were four MAGs classified as Corynebacterium frankenforstense, Proteus mirabilis, Lactobacillus johnsonii, and Bacteroides fragilis. They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.
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Affiliation(s)
- Connie A Rojas
- Genome Center, University of California-Davis, Davis, CA, USA.
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, USA.
| | - Stanley L Marks
- Department of Medicine and Epidemiology, University of California-Davis, School of Veterinary Medicine, Davis, CA, USA
| | - Eva Borras
- Department of Mechanical and Aerospace Engineering, University of California-Davis, Davis, CA, USA
- UC Davis Lung Center, University of California-Davis, Davis, CA, USA
| | - Hira Lesea
- Department of Microbiology and Molecular Genetics, University of California-Davis, Davis, CA, USA
| | - Mitchell M McCartney
- Department of Mechanical and Aerospace Engineering, University of California-Davis, Davis, CA, USA
- UC Davis Lung Center, University of California-Davis, Davis, CA, USA
- VA Northern California Health Care System, Mather, CA, USA
| | - David A Coil
- Genome Center, University of California-Davis, Davis, CA, USA
| | - Cristina E Davis
- Department of Mechanical and Aerospace Engineering, University of California-Davis, Davis, CA, USA
- UC Davis Lung Center, University of California-Davis, Davis, CA, USA
- VA Northern California Health Care System, Mather, CA, USA
| | - Jonathan A Eisen
- Genome Center, University of California-Davis, Davis, CA, USA
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California-Davis, Davis, CA, USA
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6
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Rojas CA, Marks SL, Borras E, Lesea H, McCartney MM, Coil D, Davis CE, Eisen JA. Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics. RESEARCH SQUARE 2023:rs.3.rs-2883555. [PMID: 37214811 PMCID: PMC10197813 DOI: 10.21203/rs.3.rs-2883555/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Animals rely on volatile chemical compounds for their communication and behavior. Many of these compounds are sequestered in endocrine and exocrine glands and are synthesized by anaerobic microbes. While the volatile organic compound (VOC) or microbiome composition of glandular secretions has been investigated in several mammalian species, few have linked specific bacterial taxa to the production of volatiles or to specific microbial gene pathways. Here, we use metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium, Bacteroides, Proteus, Lactobacillus, and Streptococcus, and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r=0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of these, four were inferred to have high relative abundance in metagenome profiles and had close relatives that were recovered as cultured isolates. These four MAGs were classified as Corynebacterium frankenforstense, Proteus mirabilis, Lactobacillus johnsonii, and Bacteroides fragilis. They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.
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7
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Cheng W, Xue H, Yang X, Huang D, Cai M, Huang F, Zheng L, Peng D, Thomashow LS, Weller DM, Yu Z, Zhang J. Multiple Receptors Contribute to the Attractive Response of Caenorhabditis elegans to Pathogenic Bacteria. Microbiol Spectr 2023; 11:e0231922. [PMID: 36511721 PMCID: PMC9927473 DOI: 10.1128/spectrum.02319-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/11/2022] [Indexed: 12/15/2022] Open
Abstract
Nematodes feed mainly on bacteria and sense volatile signals through their chemosensory system to distinguish food from pathogens. Although nematodes recognizing bacteria by volatile metabolites are ubiquitous, little is known of the associated molecular mechanism. Here, we show that the antinematode bacterium Paenibacillus polymyxa KM2501-1 exhibits an attractive effect on Caenorhabditis elegans via volatile metabolites, of which furfural acetone (FAc) acts as a broad-spectrum nematode attractant. We show that the attractive response toward FAc requires both the G-protein-coupled receptors STR-2 in AWC neurons and SRA-13 in AWA and AWC neurons. In the downstream olfactory signaling cascades, both the transient receptor potential vanilloid channel and the cyclic nucleotide-gated channel are necessary for FAc sensation. These results indicate that multiple receptors and subsequent signaling cascades contribute to the attractive response of C. elegans to FAc, and FAc is the first reported ligand of SRA-13. Our current work discovers that P. polymyxa KM2501-1 exhibits an attractive effect on nematodes by secreting volatile metabolites, especially FAc and 2-heptanone, broadening our understanding of the interactions between bacterial pathogens and nematodes. IMPORTANCE Nematodes feed on nontoxic bacteria as a food resource and avoid toxic bacteria; they distinguish them through their volatile metabolites. However, the mechanism of how nematodes recognize bacteria by volatile metabolites is not fully understood. Here, the antinematode bacterium Paenibacillus polymyxa KM2501-1 is found to exhibit an attractive effect on Caenorhabditis elegans via volatile metabolites, including FAc. We further reveal that the attractive response of C. elegans toward FAc requires multiple G-protein-coupled receptors and downstream olfactory signaling cascades in AWA and AWC neurons. This study highlights the important role of volatile metabolites in the interaction between nematodes and bacteria and confirms that multiple G-protein-coupled receptors on different olfactory neurons of C. elegans can jointly sense bacterial volatile signals.
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Affiliation(s)
- Wanli Cheng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hua Xue
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xue Yang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dian Huang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Feng Huang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Longyu Zheng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Linda S. Thomashow
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, Washington, USA
| | - David M. Weller
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, Washington, USA
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jibin Zhang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
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8
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Saati-Santamaría Z, Baroncelli R, Rivas R, García-Fraile P. Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution. Microbiol Spectr 2022; 10:e0237022. [PMID: 36354324 PMCID: PMC9769992 DOI: 10.1128/spectrum.02370-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
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9
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Weldon PJ, Xu S, Attygalle AB. Short-chain carboxylic acids in the scent gland secretions of the eastern small-scaled burrowing asp (Atractaspis fallax: Lamprophiidae, Serpentes, Reptilia). BIOCHEM SYST ECOL 2022. [DOI: 10.1016/j.bse.2022.104548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Ma R, Zheng W, Guo J, Hou R, Huang H, Xue F, Zhou Y, Wu W, Huang C, Gu J, Feng F, Yu X, Liu J, Li Z, Zhang L, Lan G, Chen C, Bi W, Dai Q, Owens JR, Yang H, Gu X, Yan QG, Qi D. Symbiotic microbiota and odor ensure mating in time for giant pandas. Front Microbiol 2022; 13:1015513. [PMID: 36466630 PMCID: PMC9712809 DOI: 10.3389/fmicb.2022.1015513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/27/2022] [Indexed: 06/29/2024] Open
Abstract
To achieve reproduction, male solitary mammals need to locate females using chemical communication with high levels of precision. In the case of giant pandas, the total estrus period of females was usually 15 days each year, however, successful mating activity is finished within 3 days from respective home range. The mating pattern of giant pandas, where multiple males compete for each female requires females employ efficient systems to communicate their estrus phases. To verifying whether the scent secretions of giant pandas changes by gender and estrus progression, the microbiota and compounds in 29 anogenital gland samples from 14 individuals during estrus were analyzed by 16S rRNA sequencing and GC-MS. We show that the microbiota communities covary by gender with 4 particular compounds of scent secretions. Among 597 genera, 34 were identified as biomarkers that could be used to distinguish between different estrus phases. By bacterial-compounds co-analysis, 3 fatty ester acids and squalene compounds covaried with the development of estrus in the bacterial communities of female giant pandas. This study helps clarify how a large, solitary mammal expresses accurate information to improve the likelihood of successful reproduction by changing the composition of microbiota and odor compounds of anogenital glands during estrus.
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Affiliation(s)
- Rui Ma
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | | | - Junliang Guo
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - He Huang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Fei Xue
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Yanshan Zhou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Wei Wu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Chong Huang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Jiang Gu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Feifei Feng
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Xiang Yu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Jiabin Liu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Zusheng Li
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Long Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Guanwei Lan
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Chao Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Wenlei Bi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jacob R. Owens
- Los Angeles Zoo & Botanical Gardens, Los Angeles, CA, United States
| | - Hong Yang
- Daxiangling Nature Reserve, Yaan, China
| | - Xiaodong Gu
- Sichuan Forestry and Grassland Bureau, Chengdu, China
| | - Qi-gui Yan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
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11
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Frey T, Kwadha CA, Haag F, Pelletier J, Wallin EA, Holgersson E, Hedenström E, Bohman B, Bengtsson M, Becher PG, Krautwurst D, Witzgall P. The human odorant receptor OR10A6 is tuned to the pheromone of the commensal fruit fly Drosophila melanogaster. iScience 2022; 25:105269. [PMID: 36300000 PMCID: PMC9589189 DOI: 10.1016/j.isci.2022.105269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/10/2022] [Accepted: 09/29/2022] [Indexed: 12/03/2022] Open
Abstract
All living things speak chemistry. The challenge is to reveal the vocabulary, the odorants that enable communication across phylogenies and to translate them to physiological, behavioral, and ecological function. Olfactory receptors (ORs) interface animals with airborne odorants. Expression in heterologous cells makes it possible to interrogate single ORs and to identify cognate ligands. The cosmopolitan, anthropophilic strain of the vinegar fly Drosophila melanogaster depends on human resources and housing for survival. Curiously, humans sense the pheromone (Z)-4-undecenal (Z4-11Al) released by single fly females. A screening of all human ORs shows that the most highly expressed OR10A6 is tuned to Z4-11Al. Females of an ancestral African fly strain release a blend of Z4-11Al and Z4-9Al that produces a different aroma, which is how we distinguish these fly strains by nose. That flies and humans sense Z4-11Al via dedicated ORs shows how convergent evolution shapes communication channels between vertebrate and invertebrate animals. Humans sense the sex pheromone Z411-Al released by single Drosophila melanogaster females The most highly expressed human olfactory receptor OR10A6 is tuned to Z411-Al An African fly strain emits two aldehydes, which we distinguish from Z411-Al by nose Convergent evolution shapes chemical communication between phylogenies
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Affiliation(s)
- Tim Frey
- Leibniz-Institut für Lebensmittel-Systembiologie an der Technischen Universität München, Lise-Meitner Strasse 34, 85354 Freising, Germany
| | - Charles A. Kwadha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, 234 22 Lomma, Sweden
| | - Franziska Haag
- Leibniz-Institut für Lebensmittel-Systembiologie an der Technischen Universität München, Lise-Meitner Strasse 34, 85354 Freising, Germany
| | - Julien Pelletier
- Leibniz-Institut für Lebensmittel-Systembiologie an der Technischen Universität München, Lise-Meitner Strasse 34, 85354 Freising, Germany
| | - Erika A. Wallin
- Department of Chemical Engineering, Mid Sweden University, Holmgatan 10, 85170 Sundsvall, Sweden
| | | | - Erik Hedenström
- Department of Chemical Engineering, Mid Sweden University, Holmgatan 10, 85170 Sundsvall, Sweden
| | - Björn Bohman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, 234 22 Lomma, Sweden
| | - Marie Bengtsson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, 234 22 Lomma, Sweden
| | - Paul G. Becher
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, 234 22 Lomma, Sweden
| | - Dietmar Krautwurst
- Leibniz-Institut für Lebensmittel-Systembiologie an der Technischen Universität München, Lise-Meitner Strasse 34, 85354 Freising, Germany
| | - Peter Witzgall
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, 234 22 Lomma, Sweden,Corresponding author
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12
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Fang Z, Pan T, Li L, Wang H, Zhu J, Zhang H, Zhao J, Chen W, Lu W. Bifidobacterium longum mediated tryptophan metabolism to improve atopic dermatitis via the gut-skin axis. Gut Microbes 2022; 14:2044723. [PMID: 35239463 PMCID: PMC8903757 DOI: 10.1080/19490976.2022.2044723] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Gut microbial disturbance affects allergic diseases including asthma, atopic dermatitis (AD) via the aberrant immune response. Some Bifidobacterial species and strains have been reported to improve AD via modulating immune-microbe interactions in patients. However, the effective metabolites and mechanism of alleviating AD in bifidobacteria remain to be elucidated. This study aimed to explore the microbial metabolite and mechanism of Bifidobacterium longum to improve AD. Based on shotgun metagenomic sequencing and UHPLC Q-Exactive-MS targeted metabolic experiments in vitro and in vivo, we focused on tryptophan metabolism and indole derivatives, which are endogenous ligands for aryl hydrocarbon receptor (AHR). Indole-3-carbaldehyde (I3C), a tryptophan metabolite of B. longum CCFM1029 activated AHR-mediated immune signaling pathway to improve AD symptoms in animal and clinical experiments. B. longum CCFM1029 upregulated tryptophan metabolism and increased I3C to suppress aberrant T helper 2 type immune responses, but these benefits were eliminated by AHR antagonist CH223191. Furthermore, B. longum CCFM1029 reshaped gut microbial composition in AD patients, increased fecal and serum I3C, and maintained the abundance of Lachnospiraceae related to tryptophan metabolism of gut microbiota. The results suggested that based on the interactions of the gut-skin axis, B. longum CCFM1029 upregulated tryptophan metabolism and produced I3C to activate AHR-mediated immune response, alleviating AD symptoms. Indole derivates, microbial metabolites of tryptophan, may be the potential metabolites of bifidobacteria to alleviate AD via the AHR signaling pathway.
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Affiliation(s)
- Zhifeng Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Tong Pan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Lingzhi Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jinlin Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China,(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China,(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu, China,International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, Jiangsu, China,CONTACT Wenwei Lu State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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13
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Urine Metabolomics Reveals the Effects of Confined Environment on Mating Choice in Adult Male Giant Pandas. Physiol Behav 2022; 249:113744. [DOI: 10.1016/j.physbeh.2022.113744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/20/2022] [Accepted: 02/14/2022] [Indexed: 12/19/2022]
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14
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Hu Y, Sun S, Fan H, Zhou W, Wei F. Exploring marine endosymbiosis systems with omics techniques. SCIENCE CHINA. LIFE SCIENCES 2021; 64:1013-1016. [PMID: 33860451 DOI: 10.1007/s11427-021-1925-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Yisi Hu
- CAS 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
| | - Shuyan Sun
- CAS 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
| | - Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenliang Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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