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Zhang H, Wang X, Chen A, Li S, Tao R, Chen K, Huang P, Li L, Huang J, Li C, Zhang S. Comparison of the full-length sequence and sub-regions of 16S rRNA gene for skin microbiome profiling. mSystems 2024; 9:e0039924. [PMID: 38934545 PMCID: PMC11264597 DOI: 10.1128/msystems.00399-24] [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: 03/19/2024] [Accepted: 06/02/2024] [Indexed: 06/28/2024] Open
Abstract
The skin microbiome plays a pivotal role in human health by providing protective and functional benefits. Furthermore, its inherent stability and individual specificity present novel forensic applications. These aspects have sparked considerable research enthusiasm among scholars across various fields. However, the selection of specific 16S rRNA hypervariable regions for skin microbiome studies is not standardized and should be validated through extensive research tailored to different research objectives and targeted bacterial taxa. Notably, third-generation sequencing (TGS) technology leverages the full discriminatory power of the 16S gene and enables more detailed and accurate microbial community analyses. Here, we conducted full-length 16S sequencing of 141 skin microbiota samples from multiple human anatomical sites using the PacBio platform. Based on this data, we generated derived 16S sub-region data through an in silico experiment. Comparisons between the 16S full-length and the derived variable region data revealed that the former can provide superior taxonomic resolution. However, even with full 16S gene sequencing, limitations arise in achieving 100% taxonomic resolution at the species level for skin samples. Additionally, the capability to resolve high-abundance bacteria (TOP30) at the genus level remains generally consistent across different 16S variable regions. Furthermore, the V1-V3 region offers a resolution comparable with that of full-length 16S sequences, in comparison to other hypervariable regions studied. In summary, while acknowledging the benefits of full-length 16S gene analysis, we propose the targeting of specific sub-regions as a practical choice for skin microbial research, especially when balancing the accuracy of taxonomic classification with limited sequencing resources, such as the availability of only short-read sequencing or insufficient DNA.IMPORTANCESkin acts as the primary barrier to human health. Considering the different microenvironments, microbial research should be conducted separately for different skin regions. Third-generation sequencing (TGS) technology can make full use of the discriminatory power of the full-length 16S gene. However, 16S sub-regions are widely used, particularly when faced with limited sequencing resources including the availability of only short-read sequencing and insufficient DNA. Comparing the 16S full-length and the derived variable region data from five different human skin sites, we confirmed the superiority of the V1-V3 region in skin microbiota analysis. We propose the targeting of specific sub-regions as a practical choice for microbial research.
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Affiliation(s)
- Han Zhang
- Institute of Forensic Science, Fudan University, Shanghai, China
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning, China
| | - Anqi Chen
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Shilin Li
- Institute of Forensic Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Science, Shanghai, China
| | - Kaiqin Chen
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Ping Huang
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Liliang Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jiang Huang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou, China
| | - Chengtao Li
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Suhua Zhang
- Institute of Forensic Science, Fudan University, Shanghai, China
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Coca Y, Godoy M, Pontigo JP, Caro D, Maracaja-Coutinho V, Arias-Carrasco R, Rodríguez-Córdova L, de Oca MM, Sáez-Navarrete C, Burbulis I. Bacterial networks in Atlantic salmon with Piscirickettsiosis. Sci Rep 2023; 13:17321. [PMID: 37833268 PMCID: PMC10576039 DOI: 10.1038/s41598-023-43345-x] [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] [Received: 11/01/2022] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
An unbalanced composition of gut microbiota in fish is hypothesized to play a role in promoting bacterial infections, but the synergistic or antagonistic interactions between bacterial groups in relation to fish health are not well understood. We report that pathogenic species in the Piscirickettsia, Aeromonas, Renibacterium and Tenacibaculum genera were all detected in the digesta and gut mucosa of healthy Atlantic salmon without clinical signs of disease. Although Piscirickettsia salmonis (and other pathogens) occurred in greater frequencies of fish with clinical Salmonid Rickettsial Septicemia (SRS), the relative abundance was about the same as that observed in healthy fish. Remarkably, the SRS-positive fish presented with a generalized mid-gut dysbiosis and positive growth associations between Piscirickettsiaceae and members of other taxonomic families containing known pathogens. The reconstruction of metabolic phenotypes based on the bacterial networks detected in the gut and mucosa indicated the synthesis of Gram-negative virulence factors such as colanic acid and O-antigen were over-represented in SRS positive fish. This evidence indicates that cooperative interactions between organisms of different taxonomic families within localized bacterial networks might promote an opportunity for P. salmonis to cause clinical SRS in the farm environment.
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Affiliation(s)
- Yoandy Coca
- Doctorado en Ciencias de la Ingeniería, Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, 7820436, Santiago, Región Metropolitana, Chile
| | - Marcos Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Avenida Lago Panguipulli 1390, Puerto Montt, Región de Los Lagos, Chile.
- Laboratorio Institucional, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Sede Patagonia, Avenida Lago Panguipulli 1390, Puerto Montt, Región de Los Lagos, Chile.
| | - Juan Pablo Pontigo
- Laboratorio Institucional, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Sede Patagonia, Avenida Lago Panguipulli 1390, Puerto Montt, Región de Los Lagos, Chile
| | - Diego Caro
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Avenida Lago Panguipulli 1390, Puerto Montt, Región de Los Lagos, Chile
| | - Vinicius Maracaja-Coutinho
- Centro de Modelamiento Molecular, Biofísica y Bioinformática (CM2B2), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Avenida Dr. Carlos Lorca Tobar 964, 8380494, Santiago, Región Metropolitana, Chile
- Beagle Bioinformatics, Santiago, Región Metropolitana, Chile
- Unidad de Genómica Avanzada, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Avenida Dr. Carlos Lorca Tobar 964, 8380494, Santiago, Región Metropolitana, Chile
| | - Raúl Arias-Carrasco
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Avenida Dieciocho 161, 8330383, Santiago, Región Metropolitana, Chile
| | - Leonardo Rodríguez-Córdova
- Facultad de Ingeniería, Escuela de Ingeniería, Universidad Santo Tomás, Avenida Ejército Libertador 146, Santiago, Región Metropolitana, Chile
| | - Marco Montes de Oca
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Avenida Lago Panguipulli 1390, Puerto Montt, Región de Los Lagos, Chile
| | - César Sáez-Navarrete
- Departamento de Ingeniería Química y Bioprocesos, Pontificia Universidad Católica de Chile, Avenida. Vicuña Mackenna 4860, 7820436, Santiago, Región Metropolitana, Chile.
- Centro de Investigación en Nanotecnología y Materiales Avanzados (CIEN-UC), Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, 7820436, Santiago, Región Metropolitana, Chile.
| | - Ian Burbulis
- Centro de Investigación Biomédica, Facultad de Medicina y Ciencia, Universidad San Sebastián, Sede Patagonia, Avenida Lago Panguipulli 1390, Puerto Montt, Región de Los Lagos, Chile.
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Alsamman AM, El Allali A, Mokhtar MM, Al-Sham’aa K, Nassar AE, Mousa KH, Kehel Z. AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data. PLoS One 2023; 18:e0291204. [PMID: 37729135 PMCID: PMC10511070 DOI: 10.1371/journal.pone.0291204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/23/2023] [Indexed: 09/22/2023] Open
Abstract
Multiple sequence alignment (MSA) is essential for understanding genetic variations controlling phenotypic traits in all living organisms. The post-analysis of MSA results is a difficult step for researchers who do not have programming skills. Especially those working with large scale data and looking for potential variations or variable sample groups. Generating bi-allelic data and the comparison of wild and alternative gene forms are important steps in population genetics. Customising MSA visualisation for a single page view is difficult, making viewing potential indels and variations challenging. There are currently no bioinformatics tools that permit post-MSA analysis, in which data on gene and single nucleotide scales could be combined with gene annotations and used for cluster analysis. We introduce "AlignStatPlot," a new R package and online tool that is well-documented and easy-to use for MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analyses on sequencing data and generates new visualisation methods for MSA results. When compared to currently available tools, AlignStatPlot provides a robust ability to handle and visualise diversity data, while the online version will save time and encourage researchers to focus on explaining their findings. It is a simple tool that can be used in conjunction with population genetics software.
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Affiliation(s)
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Morad M. Mokhtar
- Agricultural Genetic Engineering Research Institute, Giza, Egypt
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Khaled Al-Sham’aa
- International Center for Agriculture Research in the Dry Areas, Giza, Egypt
| | - Ahmed E. Nassar
- Agricultural Genetic Engineering Research Institute, Giza, Egypt
- International Center for Agriculture Research in the Dry Areas, Giza, Egypt
| | - Khaled H. Mousa
- Agricultural Genetic Engineering Research Institute, Giza, Egypt
- International Center for Agriculture Research in the Dry Areas, Giza, Egypt
| | - Zakaria Kehel
- International Center for Agriculture Research in the Dry Areas, Giza, Egypt
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Varliero G, Lebre PH, Stevens MI, Czechowski P, Makhalanyane T, Cowan DA. The use of different 16S rRNA gene variable regions in biogeographical studies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:216-228. [PMID: 36810880 PMCID: PMC10464692 DOI: 10.1111/1758-2229.13145] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/23/2023] [Indexed: 05/06/2023]
Abstract
16S rRNA gene amplicon sequencing is routinely used in environmental surveys to identify microbial diversity and composition of the samples of interest. The dominant sequencing technology of the past decade (Illumina) is based on the sequencing of 16S rRNA hypervariable regions. Online sequence data repositories, which represent an invaluable resource for investigating microbial distributional patterns across spatial, environmental or temporal scales, contain amplicon datasets from diverse 16S rRNA gene variable regions. However, the utility of these sequence datasets is potentially reduced by the use of different 16S rRNA gene amplified regions. By comparing 10 Antarctic soil samples sequenced for five different 16S rRNA amplicons, we explore whether sequence data derived from diverse 16S rRNA variable regions can be validly used as a resource for biogeographical studies. Patterns of shared and unique taxa differed among samples as a result of variable taxonomic resolutions of the assessed 16S rRNA variable regions. However, our analyses also suggest that the use of multi-primer datasets for biogeographical studies of the domain Bacteria is a valid approach to explore bacterial biogeographical patterns due to the preservation of bacterial taxonomic and diversity patterns across different variable region datasets. We deem composite datasets useful for biogeographical studies.
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Affiliation(s)
- Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and GenomicsUniversity of PretoriaPretoriaSouth Africa
| | - Pedro H. Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and GenomicsUniversity of PretoriaPretoriaSouth Africa
| | - Mark I. Stevens
- Securing Antarctica's Environmental FutureEarth & Biological Sciences, South Australian MuseumAdelaideAustralia
- School of Biological SciencesUniversity of AdelaideAdelaideAustralia
| | - Paul Czechowski
- Helmholtz Institute for Metabolic, Obesity and Vascular Research Leipzig (HI‐MAG)LeipzigGermany
| | - Thulani Makhalanyane
- Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
| | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and GenomicsUniversity of PretoriaPretoriaSouth Africa
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Yang K, Wang H, Luo L, Zhu S, Huang H, Wei Z, Zhu Y, Guo L, He X. Effects of different soil moisture on the growth, quality, and root rot disease of organic Panax notoginseng cultivated under pine forests. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 329:117069. [PMID: 36584512 DOI: 10.1016/j.jenvman.2022.117069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/25/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
The under-forest economy in the agroforestry system can improve land use efficiency, protect ecological environment, and promote arable land sustainable development. However, the effects of soil moisture in the forest and irrigation strategies on the healthy growth of intercropping crops are still incomplete. Here, considering the organic Panax notoginseng cultivated under pine forests (PPF) as the research object, we explored the effects of different soil moisture on the physiological state, yield, quality and disease occurrence of PPF. Our results suggested that 80-85% and 95-100% field capacity (FC) treatments were more conducive to increased photosynthetic rate and biomass accumulation of PPF, but 50-55% and 65-70% FC treatments were more conducive to the accumulation of saponins in PPF leaves. Notably, the root rot index of PPF was highest under 95-100% FC (19.51) treatment, significantly higher than that under 65-70% FC (8.44) and 80-85% FC (10.21) treatments. Further, the rhizosphere microorganisms of PPF under different soil moisture treatments were sequenced, and the sequencing data analysis revealed that high soil moisture (95-100% FC) could destroy the microbial diversity balance and cause the accumulation of pathogens (Fusarium oxysporum and Ilyonectria radicicola), leading to a high incidence of root rot. The incidence of PPF root rot was negatively correlated with rhizosphere microbial diversity. Overall, our results highlight that the quantitative irrigation (80-85% FC) is conducive to maintaining the balance between yield, saponin content and disease occurrence of PPF, providing a practical basis for PPF irrigation strategy and promoting the sustainable development of PPF agroforestry system.
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Affiliation(s)
- Kuan Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Huiling Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Lifen Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Hongping Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Zhaoxia Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Liwei Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China; Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, Yunnan, 650224, China.
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Rieder J, Kapopoulou A, Bank C, Adrian-Kalchhauser I. Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems. ENVIRONMENTAL MICROBIOME 2023; 18:8. [PMID: 36788626 PMCID: PMC9930364 DOI: 10.1186/s40793-023-00459-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/02/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Microbial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems. RESULTS We compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria. CONCLUSION The different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.
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Affiliation(s)
- Jessica Rieder
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, Institute for Fish and Wildlife Health, University of Bern, Länggasstrasse 122, 3001 Bern, Switzerland
- Division of Theoretical Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Adamandia Kapopoulou
- Division of Theoretical Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Claudia Bank
- Division of Theoretical Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Irene Adrian-Kalchhauser
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, Institute for Fish and Wildlife Health, University of Bern, Länggasstrasse 122, 3001 Bern, Switzerland
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Gao K, Geng C. Comparison of rectum fecal bacterial community of finishing bulls fed high-concentrate diets with active dry yeast and yeast culture supplementation. Anim Biosci 2023; 36:63-74. [PMID: 36108683 PMCID: PMC9834660 DOI: 10.5713/ab.22.0215] [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: 05/29/2022] [Accepted: 08/14/2022] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE The objective of this study was to investigate the effects of feeding active dry yeast (ADY) and yeast culture (YC) on fecal bacterial community in finishing bulls fed high-concentrate diets in the same experimental environment. METHODS Forty-five healthy finishing cattle (Simmental×Chinese Luxi yellow bulls; 24 months; 505±29 kg) were randomly divided into three groups: i) CON group (control group, only fed basal diet), ii) ADY group (fed basal diet + active dry yeast), and iii) YC group (fed basal diet + yeast culture). At the end of the trial, nine rectum fecal samples were randomly selected from each group for bacterial DNA sequencing. RESULTS There was no difference among groups about alpha diversity indices (all p>0.05), including ACE, Chao 1, Shannon, and Simpson indices. Principal component analysis and non-metric multidimensional scaling analysis showed a high similarity among three groups. Compared with CON group, ADY and YC groups had greater relative abundance of c_Clostridia, o_Oscillospirales, and f_Oscillospiraceae, but lesser relative abundance of g_Megasphaera, and s_Megasphaera_elsdenii (all p<0.01). And, the relative abundances of p_Firmicutes (p = 0.03), s_Prevotella_sp (p = 0.03), o_Clostridiales (p<0.01), g_Clostridium (p<0.01), f_Caloramatoraceae (p<0.01), and f_Ruminococcaceae (p = 0.04) were increased in the ADY group. The PICRUSt2 prediction results showed that the metabolic pathways had no significant differences among groups (p>0.05). Besides, the relative abundance of c_Clostridia (r = 0.42), and f_Oscillospiraceae (r = 0.40) were positively correlated to average daily gain of finishing bulls (p<0.05). CONCLUSION Both of ADY and YC had no effect on diversity of fecal bacteria in finishing bulls, but the supplementation of ADY and YC can improve the large intestinal function in finishing bulls by increasing the abundance of cellulolytic bacteria and altering the abundance of lactic acid-utilizing bacteria.
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Affiliation(s)
- Kai Gao
- Agricultural College, Yanbian University, Yanji 133000,
China,Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji 133000,
China
| | - Chunyin Geng
- Agricultural College, Yanbian University, Yanji 133000,
China,Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji 133000,
China,Corresponding Author: Chunyin Geng, E-mail:
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8
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Gao K, Geng C. Alterations in the rumen bacterial communities and metabolites of finishing bulls fed high-concentrate diets supplemented with active dry yeast and yeast culture. Front Microbiol 2022; 13:908244. [PMID: 36605509 PMCID: PMC9810264 DOI: 10.3389/fmicb.2022.908244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
This study investigated the effects of active dry yeast (ADY) and yeast culture (YC) supplementation on rumen bacteria and metabolites in finishing bulls fed high-concentrate diets using the full-length 16S rDNA gene sequencing and liquid chromatography-mass spectrometry. Supplementation with ADY improved the alpha diversity and relative abundance of rumen bacteria, while YC only affected relative abundance of rumen bacteria at the genus level. Sixty-three differential metabolites were identified in rumen fluid after ADY supplementation, and 17 after YC. PICRUSt2 functional prediction showed that ADY supplementation improved the capacity of amino acid metabolism, lipid metabolism, carbohydrate metabolism, metabolism of terpenoids and polyketides, and energy metabolism in rumen bacteria (all P < 0.05). Correlation analysis showed that the rumen differential metabolites following ADY supplementation were mainly related to Oligosphaera, Verruc, Mycoplasma, and Anaeroplasma. Supplementation with ADY was more effective than YC in remodeling the rumen bacterial flora structure and metabolite composition under high-concentrate diets.
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Affiliation(s)
- Kai Gao
- College of Agriculture, Yanbian University, Yanji, China
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji, China
| | - Chunyin Geng
- College of Agriculture, Yanbian University, Yanji, China
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji, China
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Wang Z, Zhao Y, Lan X, He J, Wan F, Shen W, Tang S, Zhou C, Tan Z, Yang Y. Tannic acid supplementation in the diet of Holstein bulls: Impacts on production performance, physiological and immunological characteristics, and ruminal microbiota. Front Nutr 2022; 9:1066074. [PMID: 36466399 PMCID: PMC9709124 DOI: 10.3389/fnut.2022.1066074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/31/2022] [Indexed: 09/29/2023] Open
Abstract
This study was conducted to evaluate the influences of supplementing tannic acid (TA) at different doses on the production performance, physiological and immunological characteristics, and rumen bacterial microbiome of cattle. Forty-eight Holstein bulls were randomly allocated to four dietary treatments: the control (CON, basal diet), the low-dose TA treatment [TAL, 0.3% dry matter (DM)], the mid-dose TA treatment (TAM, 0.9% DM), and the high-dose TA treatment (TAH, 2.7% DM). This trial consisted of 7 days for adaptation and 90 days for data and sample collection, and samples of blood and rumen fluid were collected on 37, 67, and 97 d, respectively. The average daily gain was unaffected (P > 0.05), whilst the ruminal NH3-N was significantly decreased (P < 0.01) by TA supplementation. The 0.3% TA addition lowered (P < 0.05) the levels of ruminal isobutyrate, valerate, and tumor necrosis factor alpha (TNF-α), and tended to (P < 0.1) increase the gain to feed ratio. The digestibility of DM, organic matter (OM), and crude protein, and percentages of butyrate, isobutyrate, and valerate were lower (P < 0.05), while the acetate proportion and acetate to propionate ratio in both TAM and TAH were higher (P < 0.05) than the CON. Besides, the 0.9% TA inclusion lessened (P < 0.05) the concentrations of glucagon and TNF-α, but enhanced (P < 0.05) the interferon gamma (IFN-γ) level and Simpson index of ruminal bacteria. The 2.7% TA supplementation reduced (P < 0.05) the intake of DM and OM, and levels of malondialdehyde and thyroxine, while elevated (P < 0.05) the Shannon index of the rumen bacterial populations. Moreover, the relative abundances of the phyla Fibrobacteres and Lentisphaerae, the genera Fibrobacter and Bradyrhizobium, and the species Bradyrhizobium sp., Lachnospiraceae bacterium RM29, and Lachnospiraceae bacterium CG57 were highly significantly (q < 0.01) or significantly (q < 0.05) raised by adding 2.7% TA. Results suggested that the TA addition at 0.3% is more suitable for the cattle, based on the general comparison on the impacts of supplementing TA at different doses on all the measured parameters.
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Affiliation(s)
- Zuo Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Yuan Zhao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Xinyi Lan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Fachun Wan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Weijun Shen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Shaoxun Tang
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition and Physiology and Metabolism, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Chuanshe Zhou
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition and Physiology and Metabolism, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Zhiliang Tan
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition and Physiology and Metabolism, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Yanming Yang
- Jiurui Biology and Chemistry Co., Ltd., Zhangjiajie, Hunan, China
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Hsieh YP, Hung YM, Tsai MH, Lai LC, Chuang EY. 16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences. FRONTIERS IN BIOINFORMATICS 2022; 2:905489. [PMID: 36304264 PMCID: PMC9580931 DOI: 10.3389/fbinf.2022.905489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
Analyzing 16S ribosomal RNA (rRNA) sequences allows researchers to elucidate the prokaryotic composition of an environment. In recent years, third-generation sequencing technology has provided opportunities for researchers to perform full-length sequence analysis of bacterial 16S rRNA. RDP, SILVA, and Greengenes are the most widely used 16S rRNA databases. Many 16S rRNA classifiers have used these databases as a reference for taxonomic assignment tasks. However, some of the prokaryotic taxonomies only exist in one of the three databases. Furthermore, Greengenes and SILVA include a considerable number of taxonomies that do not have the resolution to the species level, which has limited the classifiers’ performance. In order to improve the accuracy of taxonomic assignment at the species level for full-length 16S rRNA sequences, we manually curated the three databases and removed the sequences that did not have a species name. We then established a taxonomy-based integrated database by considering both taxonomies and sequences from all three 16S rRNA databases and validated it by a mock community. Results showed that our taxonomy-based integrated database had improved taxonomic resolution to the species level. The integrated database and the related datasets are available at https://github.com/yphsieh/ItgDB.
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Affiliation(s)
- Yu-Peng Hsieh
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
| | - Yuan-Mao Hung
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Liang-Chuan Lai
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
- *Correspondence: Eric Y. Chuang, ; Liang-Chuan Lai,
| | - Eric Y. Chuang
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
- College of Biomedical Engineering, China Medical University, Taichung, Taiwan
- *Correspondence: Eric Y. Chuang, ; Liang-Chuan Lai,
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11
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Fu K, Ma C, Wang C, Zhou H, Gong L, Zhang Y, Li Y. Forsythiaside A alleviated carbon tetrachloride-induced liver fibrosis by modulating gut microbiota composition to increase short-chain fatty acids and restoring bile acids metabolism disorder. Biomed Pharmacother 2022; 151:113185. [PMID: 35623173 DOI: 10.1016/j.biopha.2022.113185] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/17/2022] [Accepted: 05/22/2022] [Indexed: 11/02/2022] Open
Abstract
Liver fibrosis is a chronic and progressive disease with complex pathogenesis related to bile acids (BAs) and gut microbiota. Forsythiaside A (FTA), isolated from the traditional Chinese medicine Forsythiae Fructus (Lian Qiao), is a natural hepatoprotective agent. The purpose of this study was to investigate the protective effect of FTA on carbon tetrachloride (CCl4)-induced liver fibrosis in mice. Liver fibrosis was induced in mice by intraperitoneal injection of 2 mL/kg CCl4 three times a week for 4 weeks. FTA attenuated CCl4-induced liver fibrosis in mice, which was proved by the results of Masson and Sirius red staining, liver hydroxyproline, hyaluronic acid, laminin, type III procollagen, and type IV collagen assays. FTA inhibited hepatic stellate cell activation, and reduced hepatic inflammation and oxidative stress in mice treated with CCl4. What's more, FTA ameliorated CCl4-induced gut dysbiosis, maintained intestinal barrier function, increased the production of short-chain fatty acids (SCFAs), and improved endotoxemia, as manifested by decreased serum lipopolysaccharide levels and increased expression of ileal tight junction proteins. Besides, FTA can modulate the genes related to bile acid metabolism to alter the distribution of fecal BAs in fibrotic mice. In a word, FTA can improve liver fibrosis by inhibiting inflammation and oxidative stress, regulating gut microbiota and BA metabolism, and increasing the content of SCFAs. The results of this study provided an important reference for the study on the mechanisms by which natural products prevent liver fibrosis.
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Affiliation(s)
- Ke Fu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of Standardization for Chinese Herbal Medicine, Ministry of Education, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Cheng Ma
- State Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of Standardization for Chinese Herbal Medicine, Ministry of Education, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Cheng Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of Standardization for Chinese Herbal Medicine, Ministry of Education, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Honglin Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of Standardization for Chinese Herbal Medicine, Ministry of Education, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lihong Gong
- State Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of Standardization for Chinese Herbal Medicine, Ministry of Education, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yafang Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of Standardization for Chinese Herbal Medicine, Ministry of Education, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yunxia Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of Standardization for Chinese Herbal Medicine, Ministry of Education, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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12
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Zhao N, Guo J, Zhang B, Liu K, Liu Y, Shen Y, Li J. Heterogeneity of the Tissue-specific Mucosal Microbiome of Normal Grass Carp (Ctenopharyngodon idella). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:366-379. [PMID: 35303209 DOI: 10.1007/s10126-022-10113-3] [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: 12/13/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Microbiome plays key roles in the digestion, metabolism, and immunity of the grass carp (Ctenopharyngodon idella). Here, we characterized the normal microbiome of the intestinal contents (IC), skin mucus (SM), oral mucosa (OM), and gill mucosa (GM) of the grass carp, as well as the microbiome of the sidewall (SW) of the raising pool, using full-length 16S rRNA sequencing based on the PacBio platform in this specie for the first time. Twenty phyla, 38 classes, 130 families, 219 genera, and 291 species were classified. One hundred four common classified species might be core microbiota of grass carp. Proteobacteria, Bacteroides, and Cyanobacteria were the dominant phyla in the niche of grass carp. Proteobacteria and Bacteroides dominated the taxonomic composition in the SM, GM, and OM, while Proteobacteria, Planctomycetota, and Cyanobacteria preponderated in the IC and SW groups. Microbiota of IC exhibited higher alpha diversity indices. The microbial communities clustered either in SW or the niche from grass carp, significantly tighter in the SW, based on Bray-Curtis distances (P < 0.05). SM, GM, and OM were similar in microbial composition but were significantly different from IC and SW, while IC had similarity with SW due to their common Cyanobacteria (P < 0.05). Differences were also reflected by niche-specific and differentially abundant microorganisms such as Noviherbaspirillum in the SM and Rhodopseudomonas palustris, Mycobacterium fortuitum, and Acinetobacter schindleri in GM. Significantly raised gene expression was found in IC and SM associated with cell cycle control, cell division, chromosome, coenzyme transport and metabolism, replication, recombination and repair, cell motility, post-translational modification, signal transduction mechanisms, intracellular trafficking, secretion, and vesicles by PICRUSt. This work may be of great value for understanding of fish-microbial co-workshops, especially in different niche of grass carp.
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Affiliation(s)
- Na Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Jiamin Guo
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Bo Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Kai Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Yuting Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
- College of Fisheries and Life Science, Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
- College of Fisheries and Life Science, Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China.
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13
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Bajagai YS, Trotter M, Williams TM, Costa DFA, Whitton MM, Ren X, Wilson CS, Stanley D. The role of microbiota in animal health and productivity: misinterpretations and limitations. ANIMAL PRODUCTION SCIENCE 2022. [DOI: 10.1071/an21515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Mei S, Zhao M, Liu Y, Zhao C, Xu H, Fang Y, Zhu B. Evaluations and comparisons of microbial diversities in four types of body fluids based on two 16S rRNA gene sequencing methods. Forensic Sci Int 2021; 331:111128. [PMID: 34959019 DOI: 10.1016/j.forsciint.2021.111128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Body fluids are one of the common biological traces at crime scenes. Understanding the types of these biological traces could provide key clues for the investigations of the forensic cases. In recent years, partial hypervariable regions of 16S rRNA gene sequencing and full-length 16S rRNA gene sequencing have attracted the interests of researchers and we intend to explore which method can be better applied to forensic researches. METHODS In this study, the 16S rRNA gene V3-V4 (short-read) sequencing based on next-generation sequencing and the full-length 16S rRNA gene sequencing based on single molecule real-time sequencing were used to classify microbes in saliva, peripheral blood, vaginal secretion and menstrual blood samples. RESULTS Alpha diversity metrics in short-read sequencing were larger than those of full-length sequencing. Phylum-level bacteria in four kinds of body fluids obtained from the two platforms were similar, while their abundances were different. The results of principal coordinates analysis and analysis of molecular variance indicated the microbial compositions of vaginal secretion and menstrual blood samples were similar, and the microbial compositions among saliva, peripheral blood, vaginal secretion or menstrual blood samples were significantly different. The linear discriminant analysis effect size showed the differential bacteria screened among the four kinds of body fluids were variant in two sequencing results. CONCLUSION Both sequencing methods could be used to detect bacterial diversities in four different types of body fluids and provide potential tools for microbes to identify the four kinds of body fluids in forensic investigation, in which full-length sequencing could provide more accurate taxonomy.
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Affiliation(s)
- Shuyan Mei
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China
| | - Ming Zhao
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China
| | - Yanfang Liu
- School of Nursing, Guangdong Medical University, Dongguan 523808, P. R. China
| | - Congying Zhao
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China
| | - Hui Xu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China
| | - Yating Fang
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China
| | - Bofeng Zhu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China.
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15
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Lee H, Jeong J, Oh Y, Lee CJ, Mun S, Lee DG, Jo H, Heo YM, Baek C, Heo CY, Kang SM, Han K. Comparative analysis of human facial skin microbiome between topical sites compared to entire face. Genes Genomics 2021; 43:1483-1495. [PMID: 34734352 DOI: 10.1007/s13258-021-01180-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Skin is an essential outer barrier and supports the growth of commensal microorganisms that protects a host from the offense of foreign toxic organisms. With the rapid development of next-generation sequencing (NGS)-based applications, skin microbiome research for facial health care has reached industry growth, such as therapy and cosmetic product development. Despite the acceleration of skin microbiome research, experimental standardization protocol has not yet been established in the facial site and method of sampling. OBJECTIVE Thus, we aimed to investigate the differences in microbial composition at each facial site (cheek, mouth, forehead, and entire face) using comprehensive microbiome analysis. METHODS Twelve specimens from three men (four specimens per one person) were collected. The hypervariable regions (V3-V4) of the bacterial 16S rRNA gene were targeted for 16S amplicon library construction and classification of bacterial taxonomy. Skin microbial composition for all specimens was investigated, and the differences site-by-site in skin microbial composition were analyzed and evaluated by the various statistical tests. RESULTS We were able to validate the independent correlation between the skin microbiome composition and the facial sites. The cheek site showed the highest alpha-diversity in richness and evenness scores compared to the forehead and mouth. The cheek and mouth sites showed a positive correlation (R2 value > 0.93) with the entire face, while the forehead sites were negatively correlated (R2 value < 0.2). Given the relative abundance based on statistical correlation analysis, we estimated that the cheek site could be considered an optimal topical site to replace the entire face. CONCLUSION Our study suggests that skin microbiome profiling of four facial sites confirms that the cheek shows the most similar skin flora with the entire face. This study would be informative for preventing bias caused by sampling methods before researching and understanding skin cosmetics development or skin diseases.
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Affiliation(s)
- Haeun Lee
- Department of Bioconvergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Jinuk Jeong
- Department of Bioconvergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Yunseok Oh
- Department of Bioconvergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Cherl-Jun Lee
- Department of Bioconvergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Dong-Geol Lee
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - HyungWoo Jo
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Young Mok Heo
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Chaeyun Baek
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Chan Yeong Heo
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Bundang-gu, Seongnam, 13620, Republic of Korea.,H&BIO Corporation/R&D CENTER, Bundang-gu, Seongnam, 13605, Republic of Korea
| | - So Min Kang
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Bundang-gu, Seongnam, 13620, Republic of Korea.,H&BIO Corporation/R&D CENTER, Bundang-gu, Seongnam, 13605, Republic of Korea
| | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea. .,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. .,Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
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16
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Chae SJ, Kim EJ, Chang HC. A novel NADH fluorescence‐based method for identifying and monitoring lactic acid bacteria growths in kimchi. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.14935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- So Jeong Chae
- Department of Food and Nutrition Kimchi Research Center Chosun University 309 Pilmun‐daero, Dong‐gu Gwangju501‐759Korea
| | - Eun Jeong Kim
- Department of Refrigerator RD/ED Home Appliance & Air Solution Company, LG Electronics 170 Seongsanpaechong‐ro, Seongsan‐gu Changwon‐si, Gyeongsangnam‐do Korea
| | - Hae Choon Chang
- Department of Food and Nutrition Kimchi Research Center Chosun University 309 Pilmun‐daero, Dong‐gu Gwangju501‐759Korea
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Wang H, Zhang C, Cheng P, Wang Y, Liu H, Wang H, Wang H, Gong M. Differences in the intestinal microbiota between insecticide-resistant and -sensitive Aedes albopictus based on full-length 16S rRNA sequencing. Microbiologyopen 2021; 10:e1177. [PMID: 33970535 PMCID: PMC8087943 DOI: 10.1002/mbo3.1177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/08/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal symbiotic bacteria of Aedes albopictus play a potential role in host resistance to insecticides. In this study, we sequenced the full‐length of 16S rRNA and analyzed the differences in the intestinal microbiota between deltamethrin‐resistant and ‐sensitive Ae. albopictus. Symbiotic bacteria were cultured and analyzed using six types of culture media in aerobic and anaerobic environments. We found significant differences in the diversity and abundance of the intestinal microbiota of the two strains of Ae. albopictus. The symbiotic bacteria cultured in vitro were found to be mainly facultative anaerobes. The cultured bacteria such as Serratia oryzae and Acinetobacter junii may function to promote the development of insecticide resistance. This work indicates that intestinal bacteria may contribute to the enhancement of insecticide resistance of Ae. albopictus It also highlights the analytical advantage of full‐length 16S rRNA sequencing to study the intestinal microbiota of mosquitoes.
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Affiliation(s)
- Haiyang Wang
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Chongxing Zhang
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Peng Cheng
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Yang Wang
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Hongmei Liu
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Haifang Wang
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Huaiwei Wang
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Maoqing Gong
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
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Molecular mechanisms of heavy metals resistance of Stenotrophomonas rhizophila JC1 by whole genome sequencing. Arch Microbiol 2021; 203:2699-2709. [PMID: 33715030 DOI: 10.1007/s00203-021-02271-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 03/04/2021] [Indexed: 10/21/2022]
Abstract
In this study, a higher metal ions-resistant bacterium, Stenotrophomonas rhizophila JC1 was isolated from contaminated soil in Jinchang city, Gansu Province, China. The Pb2+ (120 mg/L) and Cu2+ (80 mg/L) removal rate of the strain reached at 76.9% and 83.4%, respectively. The genome comprises 4268161 bp in a circular chromosome with 67.52% G + C content and encodes 3719 proteins. The genome function analysis showed czc operon, mer operon, cop operon, arsenic detoxification system in strain JC1 were contributed to the removal of heavy metals. Three efflux systems (i.e., RND, CDF, and P-ATPase) on strain JC1 genome could trigger the removal of divalent cations from cells. cAMP pathway and ABC transporter pathway might be involved in the transport and metabolism of heavy metals. The homology analysis exhibited multi-gene families such as ABC transporters, heavy metal-associated domain, copper resistance protein, carbohydrate-binding domain were distributed across 410 orthologous groups. In addition, heavy metal-responsive transcription regulator, thioredoxin, heavy metal transport/detoxification protein, divalent-cation resistance protein CutA, arsenate reductase also played important roles in the heavy metals adsorption and detoxification process. The complete genome data provides insight into the exploration of the interaction mechanism between microorganisms and heavy metals.
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Wang Z, Yu Y, Li X, Xiao H, Zhang P, Shen W, Wan F, He J, Tang S, Tan Z, Wu D, Yao H. Fermented Soybean Meal Replacement in the Diet of Lactating Holstein Dairy Cows: Modulated Rumen Fermentation and Ruminal Microflora. Front Microbiol 2021; 12:625857. [PMID: 33584627 PMCID: PMC7879537 DOI: 10.3389/fmicb.2021.625857] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/07/2021] [Indexed: 12/20/2022] Open
Abstract
This study was conducted to examine the influences of replacing soybean meal (SBM) with fermented soybean meal (FSBM) in the diet of lactating Holstein cattle on rumen fermentation and ruminal bacterial microbiome. Twenty-four lactating Chinese Holstein dairy cattle were assigned to each of the two treatments in a completely randomized design: the SBM group [the basal total mixed ration (TMR) diet containing 5.77% SBM] and the FSBM group (the experimental TMR diet containing 5.55% FSBM). This trial lasted for 54 days (14 days for adjustment and 40 days for data and sample collection), and samples of rumen liquid were collected on 34 d and 54 d, respectively. The results showed that replacing SBM with FSBM significantly increased the molar percentages of propionate (P < 0.01) and valerate (P < 0.05), but reduced the total volatile fatty acid (TVFA) concentration (P < 0.05), butyrate molar proportion (P < 0.05), and the acetate to propionate ratio (P < 0.01). The copy numbers of total bacteria (P < 0.05), Fibrobacter succinogenes (P < 0.01), Selenomonas ruminantium (P < 0.01), and Prevotella spp. (P < 0.05) in the FSBM group were greater, while the density of Prevotella ruminicola (P < 0.05) was lower than those in the SBM treatment. Additionally, Succiniclasticum ruminis and Saccharofermentans acetigenes were significantly enriched (P < 0.05) in the rumen fluid of FSBM-fed cows, despite the fact that there was no remarkable difference in the Alpha diversity indexes, structure and KEGG pathway abundances of the bacterial community across the two treatments. It could hence be concluded that the substitution of FSBM for SBM modulated rumen fermentation and rumen bacterial microbiota in lactating Holstein dairy cows. Further research is required to elucidate the relevant mechanisms of FSBM, and provide more insights into the application of FSBM in dairy cattle.
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Affiliation(s)
- Zuo Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yuannian Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xinyao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Hongyan Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Peihua Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Weijun Shen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Fachun Wan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Shaoxun Tang
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition & Physiology and Metabolism, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Zhiliang Tan
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition & Physiology and Metabolism, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Duanqin Wu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Hui Yao
- Nanshan Dairy Co., Ltd., Shaoyang, China
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20
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Jeong J, Yun K, Mun S, Chung WH, Choi SY, Nam YD, Lim MY, Hong CP, Park C, Ahn YJ, Han K. The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology. Sci Rep 2021; 11:1727. [PMID: 33462291 PMCID: PMC7814050 DOI: 10.1038/s41598-020-80826-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
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Affiliation(s)
- Jinuk Jeong
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea
| | - Kyeongeui Yun
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Won-Hyong Chung
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Song-Yi Choi
- Department of Pathology, School of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Young-do Nam
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea.,Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Mi Young Lim
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Chang Pyo Hong
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - ChanHyeok Park
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - Yong Ju Ahn
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea.
| | - Kyudong Han
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. .,Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
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21
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Palmer R, Fleming GTA, Glaeser S, Semmler T, Flamm A, Ewers C, Kämpfer P, Budich O, Berrow S, O'Brien J, Siebert U, Collins E, Ruttledge M, Eisenberg T. Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon. DISEASES OF AQUATIC ORGANISMS 2020; 139:161-174. [PMID: 32406871 DOI: 10.3354/dao03478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.
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Affiliation(s)
- Roy Palmer
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway H91TK33, Ireland
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22
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Zou S, Gong L, Khan TA, Pan L, Yan L, Li D, Cao L, Li Y, Ding X, Yi G, Sun Y, Hu S, Xia L. Comparative analysis and gut bacterial community assemblages of grass carp and crucian carp in new lineages from the Dongting Lake area. Microbiologyopen 2020; 9:e996. [PMID: 32175674 PMCID: PMC7221430 DOI: 10.1002/mbo3.996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 12/17/2022] Open
Abstract
Gut microbiota are known to play an important role in health and nutrition of the host and have been attracting an increasing attention. Farming of new lineages of grass carp and crucian carp has been developed rapidly as these species were found to outperform indigenous ones in terms of growth rate and susceptibility to diseases. Despite this rapid development, no studies have addressed the characteristics of their gut microbiota as a potential factor responsible for the improved characteristics. To reveal whether microbiomes of the new lineages are different from indigenous ones, and therefore could be responsible for improved growth features, intestinal microbiota from the new lineages were subjected to high-throughput sequencing. While the phyla Firmicutes, Fusobacteria and Proteobacteria were representing the core bacterial communities that comprised more than 75% in all fish intestinal samples, significant differences were found in the microbial community composition of the new linages versus indigenous fish populations, suggesting the possibility that results in the advantages of enhanced disease resistance and rapid growth for the new fish lineages. Bacterial composition was similar between herbivorous and omnivorous fish. The relative abundance of Bacteroidetes and Actinobacteria was significantly higher in omnivores compared to that of herbivores, whereas Cetobacterium_sp. was abundant in herbivores. We also found that the gut microbiota of freshwater fish in the Dongting lake area was distinct from those of other areas. Network graphs showed the reduced overall connectivity of gut bacteria in indigenous fish, whereas the bacteria of the new fish lineage groups showed hubs with more node degree. A phylogenetic investigation of communities by reconstruction of unobserved states inferred function profile showed several metabolic processes were more active in the new lineages compared to indigenous fish. Our findings suggest that differences in gut bacterial community composition may be an important factor contributing to the rapid growth and high disease resistance of the new fish lineages.
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Affiliation(s)
- Sheng Zou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liang Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Tahir Ali Khan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Lifei Pan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liang Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Dongjie Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Lina Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Yanping Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Xuezhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Ganfeng Yi
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Yunjun Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Shengbiao Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
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23
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Klemetsen T, Willassen NP, Karlsen CR. Full-length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis. Microbiologyopen 2019; 8:e898. [PMID: 31271529 PMCID: PMC6813439 DOI: 10.1002/mbo3.898] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 12/12/2022] Open
Abstract
Understanding fish-microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community associated with the rearing systems and fish surfaces. Accurate methods to generate and analyze these microbial communities would be an important tool to help improve understanding of microbial effects in the industry. In this study, we performed taxonomic classification and determination of operational taxonomic units on Atlantic salmon microbiota by taking advantage of full-length 16S rRNA gene sequences. Skin mucus was dominated by the genera Flavobacterium and Psychrobacter. Intestinal samples were dominated by the genera Carnobacterium, Aeromonas, Mycoplasma and by sequences assigned to the order Clostridiales. Applying Sanger sequencing on the full-length bacterial 16S rRNA gene from the pool of 46 isolates obtained in this study showed a clear assignment of the PacBio full-length bacterial 16S rRNA gene sequences down to the genus level. One of the bottlenecks in comparing microbial profiles is that different studies use different 16S rRNA gene regions. Comparisons of sequence assignments between full-length and in silico derived variable 16S rRNA gene regions showed different microbial profiles with variable effects between phylogenetic groups and taxonomic ranks.
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Affiliation(s)
- Terje Klemetsen
- Department of Chemistry, Center for Bioinformatics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Nils Peder Willassen
- Department of Chemistry, Center for Bioinformatics, UiT The Arctic University of Norway, Tromsø, Norway
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