The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations
Tóm tắt
Từ khóa
Tài liệu tham khảo
LH Taylor, 2001, Risk factors for human disease emergence, Philos Trans R Soc Lond B Biol Sci, 356, 983, 10.1098/rstb.2001.0888
MEJ Woolhouse, 2002, Population biology of emerging and re-emerging pathogens, Trends in Microbiology, 10, S3, 10.1016/S0966-842X(02)02428-9
HL DuPont, 2007, The growing threat of foodborne bacterial enteropathogens of animal origin, Clinical Infectious Diseases, 45, 1353, 10.1086/522662
E Scallan, 2011, Foodborne illness acquired in the United States-major pathogens, Emerg Infect Dis, 17, 7, 10.3201/eid1701.P11101
RL Scharff, 2012, Economic Burden from Health Losses Due to Foodborne Illness in the United States, Journal of Food Protection, 75, 123, 10.4315/0362-028X.JFP-11-058
I Gabriel, 2006, Microflora of the digestive tract: critical factors and consequences for poultry, World’s Poultry Science Journal, 62, 499
BB Oakley, 2012, Pyrosequencing-based validation of a simple cell-suspension polymerase chain reaction assay for <italic>Campylobacter</italic> with application of high-processivity polymerase and novel internal amplification controls for rapid and specific detection, Diagnostic Microbiology and Infectious Disease, 72, 131, 10.1016/j.diagmicrobio.2011.11.001
BB Oakley, 2012, Application of high-throughput sequencing to measure the performance of commonly used selective cultivation methods for the foodborne pathogen <italic>Campylobacter</italic>, FEMS Microbiology Ecology, 79, 327, 10.1111/j.1574-6941.2011.01219.x
Danzeisen JL, Kim HB, Isaacson RE, Tu ZJ, Johnson TJ (2011) Modulations of the Chicken Cecal Microbiome and Metagenome in Response to Anticoccidial and Growth Promoter Treatment. PLoS One 6.
B Hald, 2004, Flies and <italic>Campylobacter</italic> infection of broiler flocks, Emerging infectious diseases, 10, 1490, 10.3201/eid1008.040129
PS Kwan, 2008, Molecular epidemiology of <italic>Campylobacter jejuni</italic> populations in dairy cattle, wildlife, and the environment in a farmland area, Applied and Environmental Microbiology, 74, 5130, 10.1128/AEM.02198-07
DG Newell, 2003, Sources of <italic>Campylobacter</italic> colonization in broiler chickens, Applied and Environmental Microbiology, 69, 4343, 10.1128/AEM.69.8.4343-4351.2003
WF Jacobs-Reitsma, 1995, Epidemiology of <italic>Campylobacter</italic> spp. at two Dutch broiler farms, Epidemiology and infection, 114, 413, 10.1017/S0950268800052122
MD Lee, 2006, <italic>Campylobacter</italic> in poultry: filling an ecological niche, Avian diseases, 50, 1, 10.1637/7474-111605R.1
MN Skov, 2004, The role of litter beetles as potential reservoir for <italic>Salmonella enterica</italic> and thermophilic <italic>Campylobacter</italic> spp. between broiler flocks, Avian Diseases, 48, 9, 10.1637/5698
R Rittenberry, 2011, Farm-to-fork safety. The new federal food safety law aims to prevent contamination rather than simply respond to it, Occupational health & safety, 80, 66
T Alter, 2011, Carry-over of thermophilic <italic>Campylobacter</italic> spp. between sequential and adjacent poultry flocks, Veterinary Microbiology, 147, 90, 10.1016/j.vetmic.2010.06.005
KL Hiett, 2002, Molecular subtype analyses of <italic>Campylobacter</italic> spp. from Arkansas and California poultry operations, Applied and Environmental Microbiology, 68, 6220, 10.1128/AEM.68.12.6220-6236.2002
JE Shreeve, 2000, Sequential spread of <italic>Campylobacter</italic> infection in a multipen broiler house, Avian Diseases, 44, 983, 10.2307/1593076
C Zweifel, 2008, Occurrence and genotypes of <italic>Campylobacter</italic> in broiler flocks, other farm animals, and the environment during several rearing periods on selected poultry farms, International Journal of Food Microbiology, 125, 182, 10.1016/j.ijfoodmicro.2008.03.038
KA Callicott, 2008, Broiler <italic>Campylobacter</italic> contamination and human campylobacteriosis in Iceland, Applied and Environmental Microbiology, 74, 6483, 10.1128/AEM.01129-08
I Damjanova, 2011, From farm to fork follow-up of thermotolerant campylobacters throughout the broiler production chain and in human cases in a Hungarian county during a ten-months period, International Journal of Food Microbiology, 150, 95, 10.1016/j.ijfoodmicro.2011.07.011
MS Rappe, 2003, The uncultured microbial majority, Annual Review of Microbiology, 57, 369, 10.1146/annurev.micro.57.030502.090759
SM Huse, 2010, Ironing out the wrinkles in the rare biosphere through improved OTU clustering, Environ Microbiol, 12, 1889, 10.1111/j.1462-2920.2010.02193.x
V Kunin, 2010, Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates, Environ Microbiol, 12, 118, 10.1111/j.1462-2920.2009.02051.x
ML Sogin, 2006, Microbial diversity in the deep sea and the underexplored “rare biosphere”, Proc Natl Acad Sci U S A, 103, 12115, 10.1073/pnas.0605127103
JT Staley, 1985, Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats, Annu Rev Microbiol, 39, 321, 10.1146/annurev.mi.39.100185.001541
KE Jones, 2008, Global trends in emerging infectious diseases, Nature, 451, 990, 10.1038/nature06536
E Scallan, 2011, Foodborne Illness Acquired in the United States-Unspecified Agents, Emerging Infectious Diseases, 17, 16, 10.3201/eid1701.P21101
J Lu, 2003, Diversity and succession of the intestinal bacterial community of the maturing broiler chicken, Appl Environ Microbiol, 69, 6816, 10.1128/AEM.69.11.6816-6824.2003
A Qu, 2008, Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome, PLoS One, 3, e2945, 10.1371/journal.pone.0002945
M Sekelja, 2012, Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal origin, Appl Environ Microbiol, 78, 2941, 10.1128/AEM.05391-11
Foster JA, Krone SM, Forney LJ (2008) Application of ecological network theory to the human microbiome. Interdisciplinary perspectives on infectious diseases 2008: Article ID 839501.
A Barberan, 2012, Using network analysis to explore co-occurrence patterns in soil microbial communities, ISME J, 6, 343, 10.1038/ismej.2011.119
K Faust, 2012, Microbial interactions: from networks to models, Nature Reviews Microbiology, 10, 538, 10.1038/nrmicro2832
JA Dickens, 1985, Automated microbiological sampling of broiler carcasses, Poultry Science, 64, 1116, 10.3382/ps.0641116
RI Griffiths, 2000, Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition, Applied and Environmental Microbiology, 66, 5488, 10.1128/AEM.66.12.5488-5491.2000
MG Wise, 2007, Quantitative analysis of the intestinal bacterial community in one- to three-week-old commercially reared broiler chickens fed conventional or antibiotic-free vegetable-based diets, J Appl Microbiol, 102, 1138
Tillman GE, Haas GJ, Wise MG, Oakley B, Smith MA, <etal>et al</etal>.. (2011) Chicken intestine microbiota following the administration of lupulone, a hop-based antimicrobial. FEMS Microbiol Ecol.
JE Line, 2013, Comparison of cumulative drip sampling with whole carcass rinses for estimation of <italic>Campylobacter</italic> species and quality indicator organisms associated with processed broiler chickens, Poultry science, 92, 218, 10.3382/ps.2012-02217
Oakley BB, Carbonero F, Dowd SE, Hawkins RJ, Purdy KJ (2011) Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter. ISME J.
PD Schloss, 2009, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl Environ Microbiol, 75, 7537, 10.1128/AEM.01541-09
SM Huse, 2007, Accuracy and quality of massively parallel DNA pyrosequencing, Genome Biol, 8, R143, 10.1186/gb-2007-8-7-r143
E Pruesse, 2007, SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Res, 35, 7188, 10.1093/nar/gkm864
JG Caporaso, 2010, PyNAST: a flexible tool for aligning sequences to a template alignment, Bioinformatics, 26, 266, 10.1093/bioinformatics/btp636
JG Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nature Methods, 7, 335, 10.1038/nmeth.f.303
T Magoc, 2011, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, 27, 2957, 10.1093/bioinformatics/btr507
D Blankenberg, 2010, Manipulation of FASTQ data with Galaxy, Bioinformatics, 26, 1783, 10.1093/bioinformatics/btq281
DAW Soergel, 2012, Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences, ISME J, 6, 1440, 10.1038/ismej.2011.208
RC Edgar, 2010, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461
W Li, 2006, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, 22, 1658, 10.1093/bioinformatics/btl158
R DCT (2010) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
T Rinttila, 2004, Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR, J Appl Microbiol, 97, 1166, 10.1111/j.1365-2672.2004.02409.x
BB Oakley, 2011, ThermoPhyl: a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples, FEMS Microbiol Ecol, 77, 17, 10.1111/j.1574-6941.2011.01079.x
W Ludwig, 2004, ARB: a software environment for sequence data, Nucleic Acids Res, 32, 1363, 10.1093/nar/gkh293
D Hermans, 2012, Poultry as a Host for the Zoonotic Pathogen <italic>Campylobacter jejuni.</italic>, Vector-Borne and Zoonotic Diseases, 12, 89, 10.1089/vbz.2011.0676
J Lu, 2003, Evaluation of broiler litter with reference to the microbial composition as assessed by using 16S rRNA and functional gene markers, Appl Environ Microbiol, 69, 901, 10.1128/AEM.69.2.901-908.2003
XY Zhu, 2002, 16S rRNA-based analysis of microbiota from the cecum of broiler chickens, Appl Environ Microbiol, 68, 124, 10.1128/AEM.68.1.124-137.2002
M Lund, 2010, Quantification of <italic>Faecalibacterium prausnitzii</italic>- and <italic>Subdoligranulum variabile</italic>-like bacteria in the cecum of chickens by real-time PCR, Poultry science, 89, 1217, 10.3382/ps.2010-00653
ME Hume, 2011, Use of pyrosequencing and denaturing gradient gel electrophoresis to examine the effects of probiotics and essential oil blends on digestive microflora in broilers under mixed <italic>Eimeria</italic> infection, Foodborne Pathog Dis, 8, 1159, 10.1089/fpd.2011.0863
NA Cox, 2001, Difficulty in recovering inoculated <italic>Campylobacter jejuni</italic> from dry poultry-associated samples, J Food Prot, 64, 252, 10.4315/0362-028X-64.2.252
AM Bojesen, 2004, In vivo studies of <italic>Gallibacterium anatis</italic> infection in chickens, Avian Pathol, 33, 145, 10.1080/03079450310001652059
J Ahn, 2011, Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison, PLoS One, 6, e22788, 10.1371/journal.pone.0022788
F Yang, 2012, Saliva microbiomes distinguish caries-active from healthy human populations, ISME J, 6, 1, 10.1038/ismej.2011.71
FM Abrahamian, 2011, Microbiology of animal bite wound infections, Clinical Microbiology Reviews, 24, 231, 10.1128/CMR.00041-10
DJ Bradshaw, 1996, Effect of oxygen, inoculum composition and flow rate on development of mixed-culture oral biofilms, Microbiology-UK, 142, 623, 10.1099/13500872-142-3-623
HS Lillard, 1993, Bactericidal effect of chlorine on attached <italic>Salmonellae</italic> with and without sonication, Journal of Food Protection, 56, 716, 10.4315/0362-028X-56.8.716
M Simmons, 2003, Comparison of sampling methods for the detection of Salmonella on whole broiler carcases purchased from retail outlets, Journal of Food Protection, 66, 1768, 10.4315/0362-028X-66.10.1768
HS Lillard, 1989, Factors affecting the persistance of <italic>Salmonella</italic> during the processing of poultry, Journal of Food Protection, 52, 829, 10.4315/0362-028X-52.11.829
M Simmons, 2008, Comparison of poultry exudate and carcass rinse sampling methods for the recovery of <italic>Campylobacter</italic> spp. subtypes demonstrates unique subtypes recovered from exudate, Journal of Microbiological Methods, 74, 89, 10.1016/j.mimet.2008.03.007
KT Young, 2007, <italic>Campylobacter jejuni</italic>: molecular biology and pathogenesis, Nat Rev Micro, 5, 665, 10.1038/nrmicro1718
K Mavromatis, 2009, Gene context analysis in the Integrated Microbial Genomes (IMG) data management system, PLoS One, 4, e7979, 10.1371/journal.pone.0007979
NJ Stern, 2001, Distribution of <italic>Campylobacter</italic> spp. in selected US poultry production and processing operations, Journal of Food Protection, 64, 1705, 10.4315/0362-028X-64.11.1705
ME Berrang, 2000, Presence and level of <italic>Campylobacter</italic> spp. on broiler carcasses throughout the processing plant, Journal of Applied Poultry Research, 9, 43, 10.1093/japr/9.1.43
Jacobs-Reitsma WF (2000) <italic>Campylobacter</italic> in the food supply. In: Nachamkin I, Blaser MJ, editors. <italic>Campylobacter</italic>. Washington, D.C.: ASM Press.
Mead GC (2000) Fresh and further-processed poultry. In: Lund BM, Baird-Parker TC, Gould GW, editors. The microbiological safety and quality of food. Gaithersburg, MD: Aspen Publishers, Inc.
AS Soerjadi, 1982, Intestinal colonization and competitive exclusion of <italic>Campylobacter fetus</italic> subsp. <italic>jejuni</italic> in young chicks, Avian Diseases, 26, 520, 10.2307/1589897
NJ Stern, 1994, Mucosal competitive exclusion to diminish colonization of chickens by <italic>Campylobacter jejuni</italic>, Poultry Science, 73, 402, 10.3382/ps.0730402
MT Khan, 2012, The gut anaerobe <italic>Faecalibacterium prausnitzii</italic> uses an extracellular electron shuttle to grow at oxic-anoxic interphases, ISME J, 6, 1578, 10.1038/ismej.2012.5
AJ Scupham, 2010, Antibiotic manipulation of intestinal microbiota to identify microbes associated with <italic>Campylobacter jejuni</italic> exclusion in poultry, Appl Environ Microbiol, 76, 8026, 10.1128/AEM.00678-10
M Hamady, 2008, Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex, Nat Methods, 5, 235, 10.1038/nmeth.1184