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Sanchez-Cid C, Keuschnig C, Torzewski K, Stachnik Ł, Kępski D, Luks B, Nawrot A, Niedzielski P, Vogel TM, Larose C. Environmental and Anthropogenic Factors Shape the Snow Microbiome and Antibiotic Resistome. Front Microbiol 2022; 13:918622. [PMID: 35783390 PMCID: PMC9245712 DOI: 10.3389/fmicb.2022.918622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Winter tourism can generate environmental pollution and affect microbial ecology in mountain ecosystems. This could stimulate the development of antibiotic resistance in snow and its dissemination through the atmosphere and through snow melting. Despite these potential impacts, the effect of winter tourism on the snow antibiotic resistome remains to be elucidated. In this study, snow samples subjected to different levels of anthropogenic activities and surrounding forest were obtained from the Sudety Mountains in Poland to evaluate the impact of winter tourism on snow bacteria using a metagenomic approach. Bacterial community composition was determined by the sequencing of the V3-V4 hypervariable region of the 16S rRNA gene and the composition of the antibiotic resistome was explored by metagenomic sequencing. Whereas environmental factors were the main drivers of bacterial community and antibiotic resistome composition in snow, winter tourism affected resistome composition in sites with similar environmental conditions. Several antibiotic resistance genes (ARGs) showed a higher abundance in sites subjected to human activities. This is the first study to show that anthropogenic activities may influence the antibiotic resistome in alpine snow. Our results highlight the need to survey antibiotic resistance development in anthropogenically polluted sites.
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Affiliation(s)
- Concepcion Sanchez-Cid
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France
- Promega France, Charbonnières-les-Bains, France
- *Correspondence: Concepcion Sanchez-Cid,
| | - Christoph Keuschnig
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France
| | - Karol Torzewski
- Department of Ecology, Biogeochemistry and Environmental Protection, Institute of Botany, Wrocław University, Wrocław, Poland
| | - Łukasz Stachnik
- Institute of Geography and Regional Development, Faculty of Earth Sciences and Environmental Management, University of Wrocław, Wrocław, Poland
| | - Daniel Kępski
- Institute of Geophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bartłomiej Luks
- Institute of Geophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Adam Nawrot
- Institute of Geophysics, Polish Academy of Sciences, Warsaw, Poland
- forScience Foundation, Toruń, Poland
| | - Przemysław Niedzielski
- Department of Analytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Timothy M. Vogel
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France
| | - Catherine Larose
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France
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Sharma V, Attri S, Mahajan R, Goel G. Microbial Profiling of Malera and Phab: Starters Used for Preparing Traditional Fermented Foods and Beverages in Himachal Pradesh, India. CURRENT NUTRITION & FOOD SCIENCE 2019. [DOI: 10.2174/1573401314666181016123558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Traditional fermented food preparation uses customary processing methods
passed on from generation to generation under natural conditions. These fermented foods use native
flora without being aware of the significant role of microbes involved in the fermentation process.
Therefore, the present study aimed to determine the bacterial composition of traditional starters used
in different fermented food preparations in Himachal Pradesh region India.
Methods:
The study investigated the bacterial DGGE (Denaturating Gradient Gel Electrophoresis)
profile targeting V3 region of 16S rRNA of two traditional starters known as Malera and Phab. The
starters are used in the preparation of fermented cereals product known as bhaturoo and alcoholic
beverages. The Shannon diversity and richness were calculated from DGGE profile. The 16S rRNA
gene sequences of identified bacterial species were deposited in NCBI database.
Results:
The DGGE profile identified eleven and seven different bacterial strains in Malera and
Phab, respectively. The Shannon diversity index of 1.07 and 0.94 was obtained for Malera and Phab,
respectively. The bacterial population was dominated by different strains of Bifidobacterium sp. in
both the starters along with the presence of non lactic enterobacteriacae members such as Klebsiella
sp. and a pathogenic strain of Dickeya chrysanthemi.
Conclusion:
The study is the first report on microbial profiling of microflora of starters. A careful
examination of individual components and method of preparation of the starters should be taken to
avoid contamination by pathogens.
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Affiliation(s)
- Vipasha Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh-173234, India
| | - Sampan Attri
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh-173234, India
| | - Rishi Mahajan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh-173234, India
| | - Gunjan Goel
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh-173234, India
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Hidden mycota of pine needles: Molecular signatures from PCR-DGGE and Ribosomal DNA phylogenetic characterization of novel phylotypes. Sci Rep 2018; 8:18053. [PMID: 30575771 PMCID: PMC6303302 DOI: 10.1038/s41598-018-36573-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 11/09/2018] [Indexed: 01/15/2023] Open
Abstract
Previous studies for enumerating fungal communities on pine needles relied entirely on phenotypic diversity (microscopy) or identification based on DNA sequence data from those taxa recovered via cultural studies. To bypass limitations of the culturing methods and provide a more realistic diversity estimate, we employed and assessed a PCR-DGGE based method coupled with rDNA phylogenetic sequence analyses to characterize fungal taxa associated with pine needles. Fresh (living) and decayed needles from three hosts of the Pinaceae (Keteleeria fortunei, Pinus elliottii and P. massoniana) were examined. Morphological studies reveal that the most abundant species associated with decayed needles were Cladosporium cladosporioides and an unidentified Trichoderma species followed by Gliocephalotrichum sp., Gliocladium sp., Lophodermium pinastri, Paecilomyces varioti, Phaeostalagmus cyclosporus and a Phoma sp, which are commonly occurring fungi. Community genomic data from freshly collected and decayed pine needles recovered 40 operational taxonomic units, which appear to be mostly undetected members of the natural fungal consortium. Sequence analyses revealed a number of phylotypes or “species” that were not recovered using traditional morphological and cultural approaches previously used. Phylogenetic data from partial 18S rDNA sequence data reveal that most phylotypes represent potential novel phylogenetic fungal lineages with affinities to the Dothideomycetes, Leotiomycetes, Lecanoromycetes and Sordariomycetes and were not identical to previously known endophytes or saprobes. Although the major ecological roles of these phylotypes in pine needles are still enigmatic, this study provides new insights in hidden fungal diversity that mycologists are possibly ignoring given the discrepancies associated with available methods. To what extent do previously recovered identified species (either as saprobes or endophytes) from morphological or culturing studies act as pioneer decomposers or constitute an integral part of endophytic community warrants further investigation.
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Wang K, Chu C, Li X, Wang W, Ren N. Succession of bacterial community function in cow manure composing. BIORESOURCE TECHNOLOGY 2018; 267:63-70. [PMID: 30014999 DOI: 10.1016/j.biortech.2018.06.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/10/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
Succession of bacterial community, metabolism function and substrate utilization capacity in 60 days composting of cow manure were analyzed by 16S rRNA pyrosequencing, PICRUSt and Biolog method, respectively. The results showed that the number of bacterial OTUs increased from 176 in raw cow manure to 203 on Day-10, 220 on Day-30 and 313 on Day-60 of the composting, respectively. The PICRUSt analysis showed that the relative abundances of genes involved in lipid and carbohydrate metabolism increased by 28.5% and 22.4% during the incubation, respectively, but the abundances of the genes involved in nucleotide and amino acid metabolism decreased by 21.6% and 2.1%. Furthermore, the average well color development (AWCD) of carboxylic acids (0.99-0.48) and amino acids (1.61-0.89) in Biolog Eco-microplate displayed a steady downtrend through the composting process. Redundancy analysis showed that ORP, moisture and temperature could explain 68.1%, 17.6% and 14.2% of the variation in bacterial genera, respectively.
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Affiliation(s)
- Ke Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, Heilongjiang 150090, China
| | - Chu Chu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, Heilongjiang 150090, China
| | - Xiangkun Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, Heilongjiang 150090, China.
| | - Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, Heilongjiang 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, Heilongjiang 150090, China
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Attri S, Mahajan R, Goel G. Development and diversity of lactic acid producing bacteria and bifidobacteria in healthy full term Indian infants from Himachal Pradesh. Intest Res 2018; 16:529-536. [PMID: 30301343 PMCID: PMC6223460 DOI: 10.5217/ir.2018.00050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/27/2018] [Indexed: 01/10/2023] Open
Abstract
Background/Aims The initial microbial colonization is a crucial step for the healthy development of an infant. Previous studies from India reported the dominance of target microbial species among Indian infants without any analysis on the diversity of target groups. This is the first study from India with an objective to investigate the establishment and diversity of lactic acid producing bacteria (LAB) and bifidobacteria in vaginally delivered, full term, breastfed infants for the first 4 months after birth. Methods Present study used polymerase chain reaction-denaturating gradient gel electrophoresis (PCR-DGGE) based sequence analysis of LAB and bifidobacteria in healthy infants. The results were used to compare the development and early colonization by LAB and bifidobacteria using diversity indices during the initial months of development of gut microbiota in infants. Results During the first 4 months, the Shannon diversity index (H) of LAB increased from 1.16 to 1.318 and for bifidobacteria the H increased from 0.975 to 1.293 (P<0.05). Higher Sorenson's pair wise similarity coefficient was observed for LAB and bifidobacteria during 2nd and the 3rd month. The species of the genera Enterococcus, Streptococcus, and Lactobacillus were dominant among the LAB group whereas Bifidobacterium breve was dominant species among Bifidobacterium group. Conclusions Our results indicate that in breast fed infants, the microbial diversity of LAB and bifidobacteria increased during the period of study.
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Affiliation(s)
- Sampan Attri
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, India
| | - Rishi Mahajan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, India
| | - Gunjan Goel
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, India
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Attri S, Sharma K, Raigond P, Goel G. Colonic fermentation of polyphenolics from Sea buckthorn ( Hippophae rhamnoides ) berries: Assessment of effects on microbial diversity by Principal Component Analysis. Food Res Int 2018; 105:324-332. [DOI: 10.1016/j.foodres.2017.11.032] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/15/2017] [Accepted: 11/19/2017] [Indexed: 12/25/2022]
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