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Horváthová T, Lafuente E, Bartels J, Wallisch J, Vorburger C. Tolerance to environmental pollution in the freshwater crustacean Asellus aquaticus: A role for the microbiome. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13252. [PMID: 38783543 PMCID: PMC11116767 DOI: 10.1111/1758-2229.13252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.
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Affiliation(s)
- Terézia Horváthová
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- Institute of Soil Biology and BiochemistryBiology Centre CASČeské BudějoviceCzechia
| | - Elvira Lafuente
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- Instituto Gulbenkian de CiênciaOeirasPortugal
| | | | | | - Christoph Vorburger
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- D‐USYS, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
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Cohen A, Turjeman S, Levin R, Tal S, Koren O. Comparison of canine colostrum and milk using a multi-omics approach. Anim Microbiome 2024; 6:19. [PMID: 38650014 PMCID: PMC11034113 DOI: 10.1186/s42523-024-00309-4] [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: 09/04/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND A mother's milk is considered the gold standard of nutrition in neonates and is a source of cytokines, immunoglobulins, growth factors, and other important components, yet little is known about the components of canine milk, specifically colostrum, and the knowledge related to its microbial and metabolic profiles is particularly underwhelming. In this study, we characterized canine colostrum and milk microbiota and metabolome for several breeds of dogs and examined profile shifts as milk matures in the first 8 days post-whelping. RESULTS Through untargeted metabolomics, we identified 63 named metabolites that were significantly differentially abundant between days 1 and 8 of lactation. Surprisingly, the microbial compositions of the colostrum and milk, characterized using 16S rRNA gene sequencing, were largely similar, with only two differentiating genera. The shifts observed, mainly increases in several sugars and amino sugars over time and shifts in amino acid metabolites, align with shifts observed in human milk samples and track with puppy development. CONCLUSION Like human milk, canine milk composition is dynamic, and shifts are well correlated with developing puppies' needs. Such a study of the metabolic profile of canine milk, and its relation to the microbial community, provides insights into the changing needs of the neonate, as well as the ideal nutrition profile for optimal functionality. This information will add to the existing knowledge base of canine milk composition with the prospect of creating a quality, tailored milk substitute or supplement for puppies.
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Affiliation(s)
- Alisa Cohen
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Rachel Levin
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Smadar Tal
- Koret School of Veterinary Medicine, The Hebrew University Veterinary Teaching Hospital, Hebrew University of Jerusalem, Rehovot, Israel
- Tel-Hai Academic College, Upper Galilee, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
- Kyung Hee University, Seoul, the Republic of Korea.
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Ma Y, Shi F, Qian S, Ma J. Variations in the dairy wastewater properties and bacterial diversity of each unit in membrane-enclosed anaerobic lagoon treatment process in Heilongjiang Province. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119035. [PMID: 37757687 DOI: 10.1016/j.jenvman.2023.119035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/06/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
In order to meet the land use requirements of the treated wastewater from high density polyethylene (HDPE) membrane-enclosed anaerobic lagoons, the physical and chemical properties of the wastewater in an HDPE membrane-enclosed anaerobic lagoon were measured. The total nitrogen content (TN) in wastewater treated in membrane-enclosed anaerobic lagoons is 3165 and 1510 mg/L in winter and summer respectively. The wastewater can be used as liquid organic fertilizer, partly replacing chemical fertilizer. The safety dosage of the wastewater was 21.48 t/ha for rice and 9.54 t/ha for corn, respectively. Meanwhile, the wastewater has the characteristics of high salt (conductivity>16.0 mS/cm) and high organic matter content (COD>16,900 mg/kg). Therefore, the potential negative effects of the wastewater on soil salinity and pH should be assessed. 16S rRNA was used to investigate the bacterial population structure and assess potential biological risks of land use of the wastewater. The wastewater from lagoon has the least and the most bacterial abundance in summer and winter, respectively. The bacterial diversity of wastewater samples from lagoon is the most. 21 and 24 phyla were detected in winter and summer samples respectively. Clostridium is the absolute dominant bacteria in the summer water samples and the absolute dominant bacteria is Trichococcus in winter water samples. Several animal and plant bacterial pathogens such as Campylobacter, Corynebacterium, Facklamia and Erysipelothrix can be detected in the wastewater samples. More than 70% of pathogenic bacteria such as Campylobacter, Facklamia, Erysipelothrix and Acholeplasma can be removed by lagoon in summer, but only about 99% of Corynebacterium is still in the lagoon (XYH). While more than 60% of Corynebacterium, Facklamia and Erysipelothrix are not removed in winter. So the biological risk of land use of anaerobic pond wastewater needs to be considered.
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Affiliation(s)
- Yuxin Ma
- School of Civil Engineering, Heilongjiang University, Harbin, 150080, PR China; Engineering Research Center of Rural Water Safety of Heilongjiang Province, Heilongjiang University, Harbin, 150080, PR China.
| | - Fengmei Shi
- Heilongjiang Academy of Black Soil Conservation and Utilization, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, PR China
| | - Sheng Qian
- School of Civil Engineering, Heilongjiang University, Harbin, 150080, PR China
| | - Jun Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, PR China
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Farooq A, Lee M, Han S, Jung GY, Kim SJ, Jung MY. Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential of Brachybacterium equifaecis sp. nov. isolated from horse feces. Microbiol Spectr 2023; 11:e0504822. [PMID: 37707449 PMCID: PMC10581053 DOI: 10.1128/spectrum.05048-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/31/2023] [Indexed: 09/15/2023] Open
Abstract
Brachybacterium species have been identified in various ecological niches and belong to the family Dermabacteriaceae within the phylum Actinobacteria. In this study, we isolated a novel Brachybacterium equifaecis JHP9 strain from horse feces and compared its kinetic, biochemical, and genomic features with those of other Brachybacterium strains. Moreover, comparative genomic analysis using publicly available Brachybacterium genomes was performed to determine the properties involved in their ecological adaptation and metabolic potential. Novel species delineation was determined phylogenetically through 16S rRNA gene similarity (up to 97.9%), average nucleotide identity (79.5-82.5%), average amino acid identity (66.7-75.8%), and in silico DNA-DNA hybridization (23.7-27.9) using closely related strains. This study also presents the first report of the kinetic properties of Brachybacterium species. Most of the Brachybacterium strains displayed high oxygen (K m(app) =1.6-24.2 µM) and glucose (K m(app) =0.73-1.22 µM) affinities, which may manifest niche adaptations. Various carbohydrate metabolisms under aerobic and anaerobic conditions, antibiotic resistance, mobile genetic elements, carbohydrate-active enzymes, lactic acid production, and the clustered regularly interspaced short palindromic repeats-Cas and bacteriophage exclusion systems were observed in the genotypic and/or phenotypic properties of Brachybacterium species, suggesting their genome flexibility, defense mechanisms, and adaptability. Our study contributes to the knowledge of the kinetic, physiological, and genomic properties of Brachybacterium species, including the novel JHP9 strain, which advocates for their tolerant and thriving nature in various environments, leading to their ecological adaptation. IMPORTANCE Basic physiological and genomic properties of most of the Brachybacterium isolates have been studied; however, the ability of this bacterium to adapt to diverse environments, which may demonstrate its role in niche differentiation, is to be identified yet. Therefore, here, we explored cellular kinetics, metabolic diversity, and ecological adaptation/defensive properties of the novel Brachybacterium strain through physiological and comparative genomic analysis. In addition, we presented the first report examining Brachybacterium kinetics, indicating that all strains of Brachybacterium, including the novel one, have high oxygen and glucose affinity. Furthermore, the comparative genomic analysis also revealed that the novel bacterium contains versatile genomic properties, which provide the novel bacterium with significant competitive advantages. Thus, in-depth genotypic and phenotypic analysis with kinetic properties at the species level of this genus is beneficial in clarifying its differential characteristics, conferring the ability to inhabit diverse ecological niches.
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Affiliation(s)
- Adeel Farooq
- Research Institute for Basic Sciences (RIBS), Jeju National University, Jeju, South Korea
| | - Myunglip Lee
- Department of Marine Life Science, Jeju National University, Jeju, South Korea
| | - Saem Han
- Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
| | - Gi-Yong Jung
- Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, South Korea
| | - So-Jeong Kim
- Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Man-Young Jung
- Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
- Department of Science Education, Jeju National University, Jeju, South Korea
- Jeju Microbiome Center, Jeju National University, Jeju, South Korea
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Zhang YD, Fan SJ, Zhang Z, Li JX, Liu XX, Hu LX, Knibbs LD, Dadvand P, Jalaludin B, Browning MH, Zhao T, Heinrich J, He Z, Chen CZ, Zhou Y, Dong GH, Yang BY. Association between Residential Greenness and Human Microbiota: Evidence from Multiple Countries. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:87010. [PMID: 37585351 PMCID: PMC10431502 DOI: 10.1289/ehp12186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 07/06/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Greenness, referring to a measurement of the density of vegetated land (e.g., gardens, parks, grasslands), has been linked with many human health outcomes. However, the evidence on greenness exposure and human microbiota remains limited, inconclusive, drawn from specific regions, and based on only modest sample size. OBJECTIVES We aimed to study the association between greenness exposure and human microbial diversity and composition in a large sample across 34 countries and regions. METHODS We explored associations between residential greenness and human microbial alpha-diversity, composition, and genus abundance using data from 34 countries. Greenness exposure was assessed using the normalized difference vegetation index and the enhanced vegetation index mean values in the month before sampling. We used linear regression models to estimate the association between greenness and microbial alpha-diversity and tested the effect modification of age, sex, climate zone, and pet ownership of participants. Differences in microbial composition were tested by permutational multivariate analysis of variance based on Bray-Curtis distance and differential taxa were detected using the DESeq2 R package between two greenness exposure groups split by median values of greenness. RESULTS We found that higher greenness was significantly associated with greater richness levels in the palm and gut microbiota but decreased evenness in the gut microbiota. Pet ownership and climate zone modified some associations between greenness and alpha-diversity. Palm and gut microbial composition at the genus level also varied by greenness. Higher abundances of the genera Lactobacillus and Bifidobacterium, and lower abundances of the genera Anaerotruncus and Streptococcus, were observed in people with higher greenness levels. DISCUSSION These findings suggest that residential greenness was associated with microbial richness and composition in the human skin and gut samples, collected across different geographic contexts. Future studies may validate the observed associations and determine whether they correspond to improvements in human health. https://doi.org/10.1289/EHP12186.
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Affiliation(s)
- Yi-Dan Zhang
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shu-Jun Fan
- Department of Environmental Health, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Zheng Zhang
- Department of Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Jia-Xin Li
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Xuan Liu
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Li-Xin Hu
- Department of Maternal and Child Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Luke D. Knibbs
- School of Public Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Payam Dadvand
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Bin Jalaludin
- School of Population Health, University of New South Wales, Kensington, New South Wales, Australia
| | - Matthew H.E.M. Browning
- Department of Park, Recreation, and Tourism Management, Clemson University, Clemson, South Carolina, USA
| | - Tianyu Zhao
- Institute and Clinic for Occupational, Social and Environmental Medicine, Hospital of the Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Comprehensive Pneumology Center Munich, LMU Munich, Munich, Germany
- German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany
- Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Joachim Heinrich
- Institute and Clinic for Occupational, Social and Environmental Medicine, LMU Munich, Munich, Germany
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Zhini He
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Cheng-Zhi Chen
- School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Yuanzhong Zhou
- Department of Epidemiology, School of Public Health, Zunyi Medical University, Zunyi, China
| | - Guang-Hui Dong
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Bo-Yi Yang
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
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Martinez-Hernandez JE, Berrios P, Santibáñez R, Cuesta Astroz Y, Sanchez C, Martin AJM, Trombert AN. First metagenomic analysis of the Andean condor ( Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome. PeerJ 2023; 11:e15235. [PMID: 37434868 PMCID: PMC10332357 DOI: 10.7717/peerj.15235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/28/2023] [Indexed: 07/13/2023] Open
Abstract
Background The Andean condor (Vultur gryphus) is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome. Methods This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways. Results Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with Clostridium perfringens, a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for Clostridium perfringens and Plesiomonas shigelloides, respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.
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Affiliation(s)
- J. Eduardo Martinez-Hernandez
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- CGNA (Agriaquaculture Nutritional Genomic Center), Temuco, Chile
| | - Pablo Berrios
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Región Metropolitana, Chile
| | - Rodrigo Santibáñez
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Yesid Cuesta Astroz
- Instituto Colombiano de Medicina Tropical, Universidad CES, Sabaneta, Colombia
| | - Carolina Sanchez
- Centro de Oncología de Precisión, Escuela de Medicina, Universidad Mayor, Santiago, Chile
- Advanced Genomics Core, Universidad Mayor, Santiago, Chile
| | - Alberto J. M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Annette N. Trombert
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Región Metropolitana, Chile
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Ganbat D, Oh D, Lee YJ, Lee DW, Kim SB, Chi WJ, Lee KE, Lee BH, Jung YJ, Lee JS, Lee SJ. Description of Brachybacterium sillae sp. nov., a thermophilic bacterium isolated from a hot spring. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01842-z. [PMID: 37227603 DOI: 10.1007/s10482-023-01842-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
The taxonomic position of strain EF45031T, isolated from the Neungam Carbonate hot spring, was examined using the polyphasic taxonomic approach. Strain EF45031T shared the highest percentage of 16S rRNA gene sequence with Brachybacterium nesterenkovii CIP 104813 T (97.7%). The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between strain EF45031T and the type strains B. nesterenkovii CIP 104813 T and B. phenoliresistens Phenol-AT were 77.0%, 69.15%, 21.9% and 75.73%, 68.81%, 20.5%, respectively. Phylogenomic analysis using an up-to-date bacterial core gene (UBCG) set revealed that strain EF45031T belonged to the genus Brachybacterium. Growth occurred between 25 and 50 ℃ at pH 6.0-9.0 and could tolerate salinity up to 5% (w/v). Strain had anteiso-C15:0 and anteiso-C17:0 as major fatty acids. Menaquinone-7 (MK-7) was the predominant respiratory menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, three aminolipids, and two unidentified glycolipids. The cell-wall peptidoglycan contained meso-diaminopimelic acid as a diagnostic diamino acid. The genome comprised 2,663,796 bp, with a G + C content of 70.9%. Stress-responsive periplasmic chaperone/protease coding genes were identified in the genome of EF45031T and were not detected in other Brachybacterium species. The polyphasic taxonomic properties indicate that the strain represents a novel species within the genus Brachybacterium, for which the name Brachybacterium sillae sp. nov. is proposed. The type strain is EF45031T (= KCTC 49702 T = NBRC 115869 T).
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Affiliation(s)
- Dariimaa Ganbat
- Major in Food Biotechnology and Research Center for Extremophiles and Marine Microbiology, Silla University, Busan, 46958, South Korea
| | - DoKyung Oh
- Department of Food Science and Technology, Pukyong National University, Busan, 48513, South Korea
| | - Yong-Jik Lee
- Department of Bio-Cosmetics, Seowon University, Chung-Ju, 28674, South Korea
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, 03722, South Korea
| | - Seong-Bo Kim
- Bio-Living Engineering Major, Global Leaders College, Yonsei University, Seoul, 03722, South Korea
| | - Won-Jae Chi
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Byoung-Hee Lee
- Biological Resources Research Department, National Institute of Biological Resources, Incheon, 22689, South Korea
| | - You-Jung Jung
- Biological Resources Utilization Department, National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Jung-Sook Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Korean Collection for Type Cultures, Jeongeup, 56212, South Korea
| | - Sang-Jae Lee
- Major in Food Biotechnology and Research Center for Extremophiles and Marine Microbiology, Silla University, Busan, 46958, South Korea.
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Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142522. [PMID: 36533958 PMCID: PMC9945507 DOI: 10.1128/jcm.01425-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.
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Rojas-Gätjens D, Valverde-Madrigal KS, Rojas-Jimenez K, Pereira R, Avey-Arroyo J, Chavarría M. Antibiotic-producing Micrococcales govern the microbiome that inhabits the fur of two- and three-toed sloths. Environ Microbiol 2022; 24:3148-3163. [PMID: 35621042 DOI: 10.1111/1462-2920.16082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022]
Abstract
Sloths have a dense coat on which insects, algae, and fungi coexist in a symbiotic relationship. This complex ecosystem requires different levels of control, however, most of these mechanisms remain unknown. We investigated the bacterial communities inhabiting the hair of two- (Choloepus Hoffmani) and three-toed (Bradypus variegatus) sloths and evaluated their potential for producing antibiotic molecules capable of exerting control over the hair microbiota. The analysis of 16S rRNA amplicon sequence variants (ASVs) revealed that the communities in both host species are dominated by Actinobacteriota and Firmicutes. The most abundant genera were Brevibacterium, Kocuria/Rothia, Staphylococcus, Rubrobacter, Nesterenkonia, and Janibacter. Furthermore, we isolated nine strains of Brevibacterium and Rothia capable of producing substances that inhibited the growth of common mammalian pathogens. The analysis of the biosynthetic gene clusters (BCGs) of these nine isolates suggests that the pathogen-inhibitory activity could be mediated by the presence of siderophores, terpenes, beta-lactones, Type III polyketide synthases (T3PKS), ribosomally synthesized, and post-translationally modified peptides (RiPPs), non-alpha poly-amino acids (NAPAA) like e-Polylysin, ectoine or nonribosomal peptides (NRPs). Our data suggest that Micrococcales that inhabit sloth hair could have a role in controlling microbial populations in that habitat, improving our understanding of this highly complex ecosystem. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | | | - Keilor Rojas-Jimenez
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Reinaldo Pereira
- Laboratorio Nacional de Nanotecnología (LANOTEC), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | | | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
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van Dorst J, Wilkins D, Crane S, Montgomery K, Zhang E, Spedding T, Hince G, Ferrari B. Microbial community analysis of biopiles in Antarctica provides evidence of successful hydrocarbon biodegradation and initial soil ecosystem recovery. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:117977. [PMID: 34416497 DOI: 10.1016/j.envpol.2021.117977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms comprise the bulk of biodiversity and biomass in Antarctic terrestrial ecosystems. To effectively protect and manage the Antarctic environment from anthropogenic impacts including contamination, the response and recovery of microbial communities should be included in soil remediation efficacy and environmental risk assessments. This is the first investigation into the microbial dynamics associated with large scale bioremediation of hydrocarbon contaminated soil in Antarctica. Over five years of active management, two significant shifts in the microbial community were observed. The initial shift at 12-24 months was significantly correlated with the highest hydrocarbon degradation rates, increased microbial loads, and significant increases in alkB gene abundances. ANCOM analysis identified bacterial genera most likely responsible for the bulk of degradation including Alkanindiges, Arthrobacter, Dietzia and Rhodococcus. The second microbial community shift occurring from 36 to 60 months was associated with further reductions in hydrocarbons and a recovery of amoA nitrification genes, but also increasing pH, accumulation of nitrite and a reduction of oligotrophic bacterial species. Over time, the addition of inorganic fertilisers altered the soil chemistry and led to a disruption of the nitrogen cycle, most likely decoupling ammonia oxidisers from nitrite oxidisers, resulting in nitrite accumulation. The results from this study provide key insights to the long-term management of hydrocarbon bioremediation in Antarctic soils.
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Affiliation(s)
- Josie van Dorst
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Australia.
| | - Daniel Wilkins
- Environmental Protection Program, Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Sally Crane
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Australia
| | - Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Australia; Evolution and Ecology Research Centre, UNSW Sydney, Australia
| | - Eden Zhang
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Australia; Evolution and Ecology Research Centre, UNSW Sydney, Australia
| | - Tim Spedding
- Environmental Protection Program, Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Greg Hince
- Environmental Protection Program, Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Belinda Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Australia; Evolution and Ecology Research Centre, UNSW Sydney, Australia.
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11
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Wiernasz N, Gigout F, Cardinal M, Cornet J, Rohloff J, Courcoux P, Vigneau E, Skírnisdottír S, Passerini D, Pilet MF, Leroi F. Effect of the Manufacturing Process on the Microbiota, Organoleptic Properties and Volatilome of Three Salmon-Based Products. Foods 2021; 10:foods10112517. [PMID: 34828798 PMCID: PMC8623285 DOI: 10.3390/foods10112517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 01/02/2023] Open
Abstract
Lightly preserved seafood products, such as cold-smoked fish and fish gravlax, are traditionally consumed in Europe and are of considerable economic importance. This work aimed to compare three products that were obtained from the same batch of fish: cold-smoked salmon (CSS) stored under vacuum packaging (VP) or a modified atmosphere packaging (MAP) and VP salmon dill gravlax (SG). Classical microbiological analyses and 16S rRNA metabarcoding, biochemical analyses (trimethylamine, total volatile basic nitrogen (TVBN), biogenic amines, pH, volatile organic compounds (VOCs)) and sensory analyses (quantitative descriptive analysis) were performed on each product throughout their storage at a chilled temperature. The three products shared the same initial microbiota, which were mainly dominated by Photobacterium, Lactococcus and Lactobacillus genera. On day 28, the VP CSS ecosystem was mainly composed of Photobacterium and, to a lesser extent, Lactococcus and Lactobacillus genera, while Lactobacillus was dominant in the MAP CSS. The diversity was higher in the SG, which was mainly dominated by Enterobacteriaceae, Photobacterium, Lactobacillus and Lactococcus. Although the sensory spoilage was generally weak, gravlax was the most perishable product (slight increase in amine and acidic off-odors and flavors, fatty appearance, slight discoloration and drop in firmness), followed by the VP CSS, while the MAP CSS did not spoil. Spoilage was associated with an increase in the TVBN, biogenic amines and spoilage associated VOCs, such as decanal, nonanal, hexadecanal, benzaldehyde, benzeneacetaldehyde, ethanol, 3-methyl-1-butanol, 2,3-butanediol, 1-octen-3-ol, 2-butanone and 1-octen-3-one. This study showed that the processing and packaging conditions both had an effect on the microbial composition and the quality of the final product.
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Affiliation(s)
- Norman Wiernasz
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
- UMR 1014, Secalim, INRAE, Oniris, 44307 Nantes, France;
| | - Frédérique Gigout
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | - Mireille Cardinal
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | - Josiane Cornet
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | - Jens Rohloff
- NTNU, Department of Biology, 7491 Trondheim, Norway;
| | | | | | - Sigurlaug Skírnisdottír
- Matıs, Research and Innovation, Exploitation and Utilization of Genetic Resources, 101-155 Reykjavik, Iceland;
| | - Delphine Passerini
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | | | - Françoise Leroi
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
- Correspondence:
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12
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Fu X, Ou Z, Zhang M, Meng Y, Li Y, Wen J, Hu Q, Zhang X, Norbäck D, Deng Y, Zhao Z, Sun Y. Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China-association with asthma, rhinitis and rhinoconjunctivitis in high school students. MICROBIOME 2021; 9:138. [PMID: 34118964 PMCID: PMC8199840 DOI: 10.1186/s40168-021-01091-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/09/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Studies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and this phenomenon is associated with urbanization and changing indoor microbiome exposure. Developing countries such as China have experienced rapid urbanization in past years, but no study has investigated microbiome exposure and urban-rural health effects in these countries. METHODS Nine high schools from urban and rural areas were randomly selected in Shanxi Province, China, and classroom vacuum dust was collected for shotgun metagenomic sequencing. A self-administered questionnaire was collected from 1332 students for personal information and health data. Three-level logistic regression was performed between microbial richness/abundance/functional pathways and the occurrence of asthma and rhinitis symptoms. RESULTS Consistent with developed countries, the prevalence of wheeze and rhinitis was higher in urban areas than in rural areas (p < 0.05). Metagenomic profiling revealed 8302 bacterial, 395 archaeal, 744 fungal, 524 protist and 1103 viral species in classroom dust. Actinobacteria (mean relative abundance 49.7%), Gammaproteobacteria (18.4%) and Alphaproteobacteria (10.0%) were the most abundant bacterial classes. The overall microbiome composition was significantly different between urban and rural schools (p = 0.001, Adonis). Species from Betaproteobactera, Gammaproteobacteria and Bacilli were enriched in urban schools, and species from Actinobacteria and Cyanobacteria were enriched in rural schools. Potential pathogens were present in higher abundance in urban schools than in rural schools (p < 0.05). Pseudoalteromonas, Neospora caninum and Microbacterium foliorum were positively associated with the occurrence of wheeze, rhinitis and rhinoconjunctivitis, and Brachybacterium was protectively (negatively) associated with rhinitis (p < 0.01). The abundance of human endocrine and metabolic disease pathways was positively associated with rhinitis (p = 0.008), and butyrate and propionate metabolic genes and pathways were significantly enriched in rural schools (p < 0.005), in line with previous findings that these short-chain fatty acids protect against inflammatory diseases in the human gut. CONCLUSIONS We conducted the first indoor microbiome survey in urban/rural environments with shotgun metagenomics, and the results revealed high-resolution microbial taxonomic and functional profiling and potential health effects. Video abstract.
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Affiliation(s)
- Xi Fu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Mei Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Yi Meng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Yanling Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Qiansheng Hu
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xin Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan, People's Republic of China
| | - Dan Norbäck
- Occupational and Environmental Medicine, Department of Medical Science, University Hospital, Uppsala University, 75237, Uppsala, Sweden
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
| | - Zhuohui Zhao
- Department of Environmental Health, School of Public Health, Fudan University, Key Laboratory of Public Health Safety of the Ministry of Education, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai Typhoon Institute/CMA, Shanghai Key Laboratory of Meteorology and Health, Shanghai, 200030, China.
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
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13
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Messman RD, Contreras-Correa ZE, Paz HA, Lemley CO. Melatonin-induced changes in the bovine vaginal microbiota during maternal nutrient restriction. J Anim Sci 2021; 99:6196023. [PMID: 33773492 DOI: 10.1093/jas/skab098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/24/2021] [Indexed: 11/14/2022] Open
Abstract
Altering the composition of the bovine vaginal microbiota has proved challenging, with recent studies deeming the microbiota dynamic due to few overall changes being found. Therefore, the objectives of this study were to determine whether gestational age, endogenous progesterone, maternal nutrient restriction, or dietary melatonin altered the composition of the bovine vaginal microbiota. Brangus heifers (n = 29) from timed artificial insemination to day 240 of gestation were used; at day 160 of gestation, heifers were assigned to either an adequate (ADQ; n = 14; 100% NRC requirements) or restricted (RES; n = 15; 60% NRC requirements) nutritional plane and were either supplemented with dietary melatonin (MEL; n = 15) or not supplemented (CON; n = 14). Samples for vaginal microbiota analysis were taken on day 0 (prior to artificial insemination), day 150 (prior to dietary treatments), and day 220 of gestation (60 d post-treatment initiation) using a double guarded culture swab. The vaginal bacterial overall community structure was determined through sequencing the V4 region of the 16S rRNA gene using the Illumina Miseq platform. Alpha diversity was compared via 2-way ANOVA; β diversity was compared via PERMANOVA. The linear discriminant analysis for effect size (LEfSe) pipeline was utilized for analysis of taxonomic rank differences between bacterial communities. Gestational age, progesterone concentration, and maternal nutritional plane did not alter α or β diversity of the vaginal microbiota. However, gestational age resulted in compositional changes at the order, family, and genus level. Moreover, dietary melatonin supplementation did not alter α diversity of the vaginal microbiota but did alter β diversity (P = 0.02). Specifically, melatonin altered the composition at the genus level and increased the prevalence of aerobic bacteria in the vaginal tract. To date, melatonin is the first hormone associated with altering the composition of the bovine vaginal microbiota.
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Affiliation(s)
- Riley D Messman
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Zully E Contreras-Correa
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Henry A Paz
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Caleb O Lemley
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
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14
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Chen MS, Li FN, Chen XH, Yan XR, Tuo L. Brachybacterium halotolerans sp. nov., a halotolerant, endophytic actinomycete isolated from branch of Bruguiera gymnoirhiza. Antonie Van Leeuwenhoek 2021; 114:875-884. [PMID: 33796984 DOI: 10.1007/s10482-021-01565-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
A novel, aerobic, moderately halophilic Gram-positive actinomycete, strain MASK1Z-5T was isolated from a surface-sterilized branch of Bruguiera gymnoirhiza in Shankou Mangrove Nature Reserve, Guangxi, China. The taxonomic position of the strain was investigated using a polyphasic approach. Strain MASK1Z-5T tolerated up to 20% (w/v) NaCl (optimum 0-7%), and grew at pH 5.0-12.0 (optimum pH 7.0-8.0), 20-37 °C (optimum 30 °C). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MASK1Z-5T belonged to the genus Brachybacterium, and showed the highest 16S rRNA gene sequence similarity of 98.0% to B. endophyticum M1HQ-2T. The cell-wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. MK-7 was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid and three unidentified lipids. The major fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The DNA G + C content was calculated to be 71.8 mol% based on the whole genome sequence. The estimated values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) based on whole genome sequences between strain MASK1Z-5T and B. endophyticum M1HQ-2T were 81.8% and 25.0%, respectively. The phenotypic, chemotaxonomic and genotypic properties clearly indicated that strain MASK1Z-5T represents a novel species within the genus Brachybacterium, for which the name Brachybacterium halotolerans sp. nov. is proposed. The type strain is MASK1Z-5T (= CGMCC1.18660T = JCM 34339T).
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Affiliation(s)
- Ming-Sheng Chen
- Life Sciences Institute, Zunyi Medical University, Zunyi, 563006, People's Republic of China
| | - Fei-Na Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Disease, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, People's Republic of China
| | - Xiao-Hui Chen
- Life Sciences Institute, Zunyi Medical University, Zunyi, 563006, People's Republic of China
| | - Xiao-Rui Yan
- Life Sciences Institute, Zunyi Medical University, Zunyi, 563006, People's Republic of China
| | - Li Tuo
- Life Sciences Institute, Zunyi Medical University, Zunyi, 563006, People's Republic of China.
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15
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Vega-Celedón P, Bravo G, Velásquez A, Cid FP, Valenzuela M, Ramírez I, Vasconez IN, Álvarez I, Jorquera MA, Seeger M. Microbial Diversity of Psychrotolerant Bacteria Isolated from Wild Flora of Andes Mountains and Patagonia of Chile towards the Selection of Plant Growth-Promoting Bacterial Consortia to Alleviate Cold Stress in Plants. Microorganisms 2021; 9:microorganisms9030538. [PMID: 33807836 PMCID: PMC7998784 DOI: 10.3390/microorganisms9030538] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 02/02/2023] Open
Abstract
Cold stress decreases the growth and productivity of agricultural crops. Psychrotolerant plant growth-promoting bacteria (PGPB) may protect and promote plant growth at low temperatures. The aims of this study were to isolate and characterize psychrotolerant PGPB from wild flora of Andes Mountains and Patagonia of Chile and to formulate PGPB consortia. Psychrotolerant strains were isolated from 11 wild plants (rhizosphere and phyllosphere) during winter of 2015. For the first time, bacteria associated with Calycera, Orites, and Chusquea plant genera were reported. More than 50% of the 130 isolates showed ≥33% bacterial cell survival at temperatures below zero. Seventy strains of Pseudomonas, Curtobacterium, Janthinobacterium, Stenotrophomonas, Serratia, Brevundimonas, Xanthomonas, Frondihabitans, Arthrobacter, Pseudarthrobacter, Paenarthrobacter, Brachybacterium, Clavibacter, Sporosarcina, Bacillus, Solibacillus, Flavobacterium, and Pedobacter genera were identified by 16S rRNA gene sequence analyses. Ten strains were selected based on psychrotolerance, auxin production, phosphate solubilization, presence of nifH (nitrogenase reductase) and acdS (1-aminocyclopropane-1-carboxylate (ACC) deaminase) genes, and anti-phytopathogenic activities. Two of the three bacterial consortia formulated promoted tomato plant growth under normal and cold stress conditions. The bacterial consortium composed of Pseudomonas sp. TmR5a & Curtobacterium sp. BmP22c that possesses ACC deaminase and ice recrystallization inhibition activities is a promising candidate for future cold stress studies.
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Affiliation(s)
- Paulina Vega-Celedón
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
- Correspondence: (P.V.-C.); (M.S.); Tel.: +56-322654685 (P.V.-C.)
| | - Guillermo Bravo
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Alexis Velásquez
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Fernanda P. Cid
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Avenida Francisco Salazar 1145, Temuco 4811230, Chile; (F.P.C.); (M.A.J.)
- Center of Plant-Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 1145, Temuco 4811230, Chile
| | - Miryam Valenzuela
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Ingrid Ramírez
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Ingrid-Nicole Vasconez
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Inaudis Álvarez
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Milko A. Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Avenida Francisco Salazar 1145, Temuco 4811230, Chile; (F.P.C.); (M.A.J.)
- Center of Plant-Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 1145, Temuco 4811230, Chile
| | - Michael Seeger
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
- Correspondence: (P.V.-C.); (M.S.); Tel.: +56-322654685 (P.V.-C.)
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16
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Madoroba E, Magwedere K, Chaora NS, Matle I, Muchadeyi F, Mathole MA, Pierneef R. Microbial Communities of Meat and Meat Products: An Exploratory Analysis of the Product Quality and Safety at Selected Enterprises in South Africa. Microorganisms 2021; 9:507. [PMID: 33673660 PMCID: PMC7997435 DOI: 10.3390/microorganisms9030507] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms.
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Affiliation(s)
- Evelyn Madoroba
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Kudakwashe Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria 0001, South Africa;
| | - Nyaradzo Stella Chaora
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida 1710, South Africa;
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (F.M.); (R.P.)
| | - Itumeleng Matle
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort 0110, South Africa; (I.M.); (M.A.M.)
| | - Farai Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (F.M.); (R.P.)
| | - Masenyabu Aletta Mathole
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort 0110, South Africa; (I.M.); (M.A.M.)
| | - Rian Pierneef
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (F.M.); (R.P.)
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Fritz B, Schäfer K, März M, Wahl S, Ziemssen F, Egert M. Eye-Catching Microbes-Polyphasic Analysis of the Microbiota on Microscope Oculars Verifies Their Role as Fomites. J Clin Med 2020; 9:jcm9051572. [PMID: 32455878 PMCID: PMC7290821 DOI: 10.3390/jcm9051572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 11/16/2022] Open
Abstract
Microscopes are used in virtually every biological and medical laboratory. Previous cultivation-based studies have suggested that direct contact with microscope eyepieces increases the risk of eye infections. To obtain a deeper insight into the microbiota on oculars, we analysed 10 recently used university microscopes. Their left oculars were used for a cultivation-based approach, while the right oculars served for massive gene sequencing. After cleaning with isopropyl alcohol, the oculars were re-sampled and analysed again. All oculars were found to be contaminated with bacteria, with a maximum load of 1.7 × 103 CFU cm-2. MALDI Biotyping revealed mainly Cutibacterium (68%), Staphylococcus (14%) and Brevibacterium (10%), with the most abundant species being Cutibacterium acnes (13%) and Staphylococcus capitis (6%). Cleaning reduced the microbial load by up to 2 log scales. Within 10 uncleaned and 5 cleaned samples, 1480 ASVs were assigned to 10 phyla and 262 genera. The dominant genera before cleaning were Cutibacterium (78%), Paracoccus (13%), Pseudomonas (2%) and Acinetobacter (1%). The bacteriota composition on the cleaned oculars was similar; however, it probably largely represented dead bacteria. In summary, used oculars were significantly contaminated with skin and environmental bacteria, including potential pathogens. Regular cleaning is highly recommended to prevent eye and skin infections.
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Affiliation(s)
- Birgit Fritz
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
| | - Karin Schäfer
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
| | - Melanie März
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
| | - Siegfried Wahl
- Carl Zeiss Vision International GmbH, Turnstrasse 27, 73430 Aalen, Germany;
- Institute for Ophthalmic Research, Eberhard-Karls University, Elfriede-Aulhorn-Strasse 7, 72076 Tuebingen, Germany
| | - Focke Ziemssen
- Center for Ophthalmology, Eberhard-Karls University, Elfriede-Aulhorn-Strasse 7, 72076 Tuebingen, Germany;
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
- Correspondence: ; Tel.: +49-7720-307-4554
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Complete Genome Sequence of Brachybacterium sp. Strain SGAir0954, Isolated from Singapore Air. Microbiol Resour Announc 2019; 8:8/32/e00619-19. [PMID: 31395638 PMCID: PMC6687925 DOI: 10.1128/mra.00619-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Brachybacterium sp. strain SGAir0954 was isolated from tropical air collected in Singapore, and its genome was sequenced and assembled using long reads generated by single-molecule real-time (SMRT) sequencing. The complete genome has a size of 3.41 Mb and consists of 2,955 protein coding genes, 50 tRNAs, and 9 rRNAs.
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Antibiotic resistance genes in the Actinobacteria phylum. Eur J Clin Microbiol Infect Dis 2019; 38:1599-1624. [PMID: 31250336 DOI: 10.1007/s10096-019-03580-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2018; 68:3379-3393. [DOI: 10.1099/ijsem.0.003071] [Citation(s) in RCA: 310] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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