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Fan L, Shuai J, Zeng R, Mo H, Wang S, Zhang X, He Y. Validation and application of quantitative PCR assays using host-specific Bacteroidales genetic markers for swine fecal pollution tracking. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:1569-1577. [PMID: 28967572 DOI: 10.1016/j.envpol.2017.09.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 06/07/2023]
Abstract
Genome fragment enrichment (GFE) method was applied to identify host-specific bacterial genetic markers that differ among different fecal metagenomes. To enrich for swine-specific DNA fragments, swine fecal DNA composite (n = 34) was challenged against a DNA composite consisting of cow, human, goat, sheep, chicken, duck and goose fecal DNA extracts (n = 83). Bioinformatic analyses of 384 non-redundant swine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode metabolism-associated, cellular processes and information storage and processing. After challenged against fecal DNA extracted from different animal sources, four sequences from the clone libraries targeting two Bacteroidales- (genes 1-38 and 3-53), a Clostridia- (gene 2-109) as well as a Bacilli-like sequence (gene 2-95), respectively, showed high specificity to swine feces based on PCR analysis. Host-specificity and host-sensitivity analysis confirmed that oligonucleotide primers and probes capable of annealing to select Bacteroidales-like sequences (1-38 and 3-53) exhibited high specificity (>90%) in quantitative PCR assays with 71 fecal DNAs from non-target animal sources. The two assays also demonstrated broad distributions of corresponding genetic markers (>94% positive) among 72 swine feces. After evaluation with environmental water samples from different areas, swine-targeted assays based on two Bacteroidales-like GFE sequences appear to be suitable quantitative tracing tools for swine fecal pollution.
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Affiliation(s)
- Lihua Fan
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Jiangbing Shuai
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou, China.
| | - Ruoxue Zeng
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou, China
| | - Hongfei Mo
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou, China
| | - Suhua Wang
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou, China
| | - Xiaofeng Zhang
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou, China
| | - Yongqiang He
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou, China
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Chen H, Zhang H, Xiong J, Wang K, Zhu J, Zhu X, Zhou X, Zhang D. Successional trajectories of bacterioplankton community over the complete cycle of a sudden phytoplankton bloom in the Xiangshan Bay, East China Sea. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 219:750-759. [PMID: 27453358 DOI: 10.1016/j.envpol.2016.07.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/13/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
Phytoplankton bloom has imposed ecological concerns worldwide; however, few studies have been focused on the successional trajectories of bacterioplankton community over a complete phytoplankton bloom cycle. Using 16S pyrosequencing, we investigated how the coastal bacterioplankton community compositions (BCCs) respond to a phytoplankton bloom in the Xiangshan Bay, East China Sea. The results showed that BCCs were significantly different among the pre-bloom, bloom, and after-bloom stages, with the lowest bacterial diversity at the bloom phase. The BCCs at the short-term after-bloom phase showed a rapid but incomplete recovery to the pre-bloom phase, evidenced by 69.8% similarity between pre-bloom and after-bloom communities. This recovery was parallel with the dynamics of the operational taxonomic units (OTUs) affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Alphaproteobacteria and Gammaproteobacteria, whose abundance enriched when bloom occur, and decreased after-bloom, and vice versa. Collectively, the results showed that the BCCs were sensitive to algal-induced disturbances, but could recover to a certain extent after bloom. In addition, OTUs which enriched or decreased during this process are closely associated with this temporal pattern, thus holding the potential to evaluate and indicate the succession stage of phytoplankton bloom.
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Affiliation(s)
- Heping Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Faculty of Architectural, Civil Engineering and Environment, Ningbo University, Ningbo, 315211, China
| | - Huajun Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Kai Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Jianlin Zhu
- Faculty of Architectural, Civil Engineering and Environment, Ningbo University, Ningbo, 315211, China
| | - Xiangyu Zhu
- Ocean and Fishery Information Monitoring Center of Ningbo, Ningbo, 315010, China
| | - Xiaoyan Zhou
- Ocean and Fishery Information Monitoring Center of Ningbo, Ningbo, 315010, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China.
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Sun D, Duan C, Shang Y, Ma Y, Tan L, Zhai J, Gao X, Guo J, Wang G. Application of Faecalibacterium 16S rDNA genetic marker for accurate identification of duck faeces. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7639-7647. [PMID: 26743644 DOI: 10.1007/s11356-015-6024-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
The aim of this study was to judge the legal duty of pollution liabilities by assessing a duck faeces-specific marker, which can exclude distractions of residual bacteria from earlier contamination accidents. With the gene sequencing technology and bioinformatics method, we completed the comparative analysis of Faecalibacterium sequences, which were associated with ducks and other animal species, and found the sequences unique to duck faeces. Polymerase chain reaction (PCR) and agarose gel electrophoresis techniques were used to verify the reliability of both human and duck faeces-specific primers. The duck faeces-specific primers generated an amplicon of 141 bp from 43.3 % of duck faecal samples, 0 % of control samples and 100 % of sewage wastewater samples that contained duck faeces. We present here the initial evidence of Faecalibacterium-based applicability as human faeces-specificity in China. Meanwhile, this study represents the initial report of a Faecalibacterium marker for duck faeces and suggests an independent or supplementary environmental biotechnology of microbial source tracking (MST).
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Affiliation(s)
- Da Sun
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China
| | - Chuanren Duan
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China.
| | - Yaning Shang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China
| | - Yunxia Ma
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China
| | - Lili Tan
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China
| | - Jun Zhai
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, College of Urban Construction and Environmental Engineering, Chongqing University, Chongqing, China
| | - Xu Gao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, College of Urban Construction and Environmental Engineering, Chongqing University, Chongqing, China
| | - Jingsong Guo
- Key Laboratory of Reservoir Aquatic Environment of CAS, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Guixue Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China.
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Araújo S, Henriques IS, Leandro SM, Alves A, Pereira A, Correia A. Gulls identified as major source of fecal pollution in coastal waters: a microbial source tracking study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 470-471:84-91. [PMID: 24140684 DOI: 10.1016/j.scitotenv.2013.09.075] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/11/2013] [Accepted: 09/24/2013] [Indexed: 06/02/2023]
Abstract
Gulls were reported as sources of fecal pollution in coastal environments and potential vectors of human infections. Microbial source tracking (MST) methods were rarely tested to identify this pollution origin. This study was conducted to ascertain the source of water fecal contamination in the Berlenga Island, Portugal. A total of 169 Escherichia coli isolates from human sewage, 423 isolates from gull feces and 334 water isolates were analyzed by BOX-PCR. An average correct classification of 79.3% was achieved. When an 85% similarity cutoff was applied 24% of water isolates were present in gull feces against 2.7% detected in sewage. Jackknifing resulted in 29.3% of water isolates classified as gull, and 10.8% classified as human. Results indicate that gulls constitute a major source of water contamination in the Berlenga Island. This study validated a methodology to differentiate human and gull fecal pollution sources in a real case of a contaminated beach.
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Affiliation(s)
- Susana Araújo
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Isabel S Henriques
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Sérgio Miguel Leandro
- GIRM, Marine Resources Research Group, School of Tourism and Maritime Technology, Polytechnic Institute of Leiria, Campus 4, 2520-641 Peniche, Portugal
| | - Artur Alves
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Anabela Pereira
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - António Correia
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Fu LL, Li JR. Microbial Source Tracking: A Tool for Identifying Sources of Microbial Contamination in the Food Chain. Crit Rev Food Sci Nutr 2013; 54:699-707. [DOI: 10.1080/10408398.2011.605231] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Jost T, Lacroix C, Braegger CP, Rochat F, Chassard C. Vertical mother-neonate transfer of maternal gut bacteria via breastfeeding. Environ Microbiol 2013; 16:2891-904. [PMID: 24033881 DOI: 10.1111/1462-2920.12238] [Citation(s) in RCA: 350] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/22/2013] [Accepted: 07/04/2013] [Indexed: 12/12/2022]
Abstract
Breast milk has recently been recognized as source of commensal and potential probiotic bacteria. The present study investigated whether viable strains of gut-associated obligate anaerobes are shared between the maternal and neonatal gut ecosystem via breastfeeding. Maternal faeces, breast milk and corresponding neonatal faeces collected from seven mothers-neonate pairs at three neonatal sampling points were analyzed by culture-independent (pyrosequencing) and culture-dependent methods (16S rRNA gene sequencing, pulsed field gel electrophoresis, random amplified polymorphic DNA and repetitive extragenic palindromic polymerase chain reaction. Pyrosequencing allowed identifying gut-associated obligate anaerobic genera, like Bifidobacterium, Bacteroides, Parabacteroides and members of the Clostridia (Blautia, Clostridium, Collinsella and Veillonella) shared between maternal faeces, breast milk and neonatal faeces. Using culture, a viable strain of Bifidobacterium breve was shown to be shared between all three ecosystems within one mother-neonate pair. Furthermore, pyrosequencing revealed that several butyrate-producing members of the Clostridia (Coprococcus, Faecalibacterium, Roseburia and Subdoligranulum) were shared between maternal faeces and breast milk. This study shows that (viable) obligate gut-associated anaerobes may be vertically transferred from mother to neonate via breastfeeding. Thus, our data support the recently suggested hypothesis of a novel way of mother-neonate communication, in which maternal gut bacteria reach breast milk via an entero-mammary pathway to influence neonatal gut colonization and maturation of the immune system.
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Affiliation(s)
- Ted Jost
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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Crab meat: a novel vehicle for E. coli O157 identified in an outbreak in South West England, August 2011. Epidemiol Infect 2012; 141:2043-50. [PMID: 23218436 DOI: 10.1017/s0950268812002816] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In August 2011, we investigated an outbreak of Escherichia coli O157 in Plymouth, England, utilizing a case-control study and food traceback. Nine cases, eight laboratory-confirmed with E. coli O157 phage type 21/28 verocytotoxin 2 and one epidemiologically linked, had onsets from 30 July 2011 to 15 August 2011. We compared cases (n=8) with controls (n=28) of similar age and sex (median age 61 vs. 55 years, females 75% vs. 61%). Cases were 58 times more likely to have eaten crab (88% vs. 11%; odds ratio 58, 95% confidence interval 4-2700). Eight cases consumed crab sourced from the same supplier who was not registered with the local authority. This outbreak pointed to crab as a possible vehicle of E. coli O157 infection. We ensured the withdrawal of crab meat sourced from unregistered suppliers from food venues by 25 August 2011. We also emphasized the importance of only using registered suppliers to the food venues. Since then no further associated cases have been reported.
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