High-throughput assessment of bacterial ecology in hog, cow and ovine casings used in sausages production

International Journal of Food Microbiology

Volumn 212, Issue , 2015, Pages 49-59

  Rebecchi, Annalisa ^a   Pisacane, Vincenza ^a   Miragoli, Francesco ^a   Polka, Justyna ^a   Falasconi, Irene ^a   Morelli, Lorenzo ^a   Puglisi, Edoardo ^a  

^a UNIVERSITÀ CATTOLICA DEL SACRO CUORE   (Italy)

Author keywords

Animal intestines; Bacterial biodiversity; Illumina; Natural casings

Indexed keywords

RNA 16S;

AEROMONADACEAE; AMPLICON; ANAEROCOCCUS; ANAEROSPHAERA AMINIPHILA; ARTICLE; BACILLUS COAGULANS; BACTERIAL COUNT; BACTERIAL GENETICS; BACTERIUM CULTURE; BACTERIUM ISOLATE; BIFIDOBACTERIUM ANIMALIS; BIFIDOBACTERIUM BREVE; CLOSTRIDIACEAE; CLOSTRIDIUM BIFERMENTANS; CLOSTRIDIUM PERFRINGENS; COLONY FORMING UNIT; CORYNEBACTERIUM; CORYNEBACTERIUM TESTUDINORIS; COW; ENTEROBACTERIACEAE; ENTEROCOCCUS FAECALIS; FOOD CONTROL; FOOD PROCESSING; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; LACTOBACILLUS AMYLOVORUS; LACTOBACILLUS CRISPATUS; LACTOBACILLUS CURVATUS; LACTOBACILLUS PARACASEI; LACTOBACILLUS PLANTARUM; LACTOBACILLUS REUTERI; LACTOBACILLUS SAKEI; LACTOBACILLUS SALIVARIUS; MEAT INDUSTRY; MOLECULAR TYPING; MORAXELLACEAE; NATURAL CASING; NONHUMAN; PEDIOCOCCUS PENTOSACEUS; PEPTONIPHILUS; PHYLOGENY; PIG; PROPIONIBACTERIUM GRANULOSUM; SHEEP; SMALL INTESTINE; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS EPIDERMIDIS; STAPHYLOCOCCUS HAEMOLYTICUS; STAPHYLOCOCCUS PASTEURI; STAPHYLOCOCCUS SAPROPHYTICUS; STAPHYLOCOCCUS SIMULANS; STAPHYLOCOCCUS XYLOSUS; VAGOCOCCUS; VIBRIONACEAE; ANIMAL; BIODIVERSITY; BOVINE; CLASSIFICATION; FEMALE; FERMENTATION; GENETICS; GRAM POSITIVE BACTERIUM; INTESTINE; ISOLATION AND PURIFICATION; MEAT; MICROBIOLOGY; PHYSIOLOGY;

ANIMALIA; BACTERIA (MICROORGANISMS); BIFIDOBACTERIUM; CLOSTRIDIUM; LACTOBACILLUS; OVIS; STAPHYLOCOCCUS; VAGOCOCCUS;

ANIMALS; BIODIVERSITY; CATTLE; FEMALE; FERMENTATION; FOOD MICROBIOLOGY; GRAM-POSITIVE BACTERIA; INTESTINES; MEAT PRODUCTS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SHEEP; SWINE;

EID: 84940446811     PISSN: 01681605     EISSN: 18793460     Source Type: Journal    
DOI: 10.1016/j.ijfoodmicro.2015.04.047     Document Type: Article

References (38)

1. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
2. Bakker W., Houben J., Koolmees P., Bindrich U., Sprehe L. Effect of initial mild curing, with additives, of hog and sheep sausage casings on their microbial quality and mechanical properties after storage at difference temperatures. Meat Sci. 1999, 51:163-174.
3. Benli H., Hafley B., Keeton J., Lucia L., Cabrera-Diaz E., Acuff G. Biomechanical and microbiological changes in natural hog casings treated with ozone. Meat Sci. 2008, 79:155-162.
4. Berry D., Mahfoudh K.B., Wagner M., Loy A. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl. Environ. Microbiol. 2011, 77:7846-7849.
5. Biddle A.S., Black S.J., Blanchard J.L. An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction. PLoS One 2013, 8:e77599.
6. Byun M., Lee J., Jo C., Yook H. Quality properties of sausage made with gamma-irradiated natural pork and lamb casing. Meat Sci. 2001, 59:223-228.
7. Cocolin L., Alessandria V., Dolci P., Gorra R., Rantsiou K. Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation. Int. J. Food Microbiol. 2013, 167:29-43.
8. Comi G., Urso R., Iacumin L., Rantsiou K., Cattaneo P., Cantoni C., Cocolin L. Characterisation of naturally fermented sausages produced in the North East of Italy. Meat Sci. 2005, 69:381-392.
9. DeSantis T.Z., Hugenholtz P., Keller K., Brodie E.L., Larsen N., Piceno Y.M., Phan R., Andersen G.L. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 2006, 34:394-399.
10. Dicello F., Fani R. A molecular strategy for the study of natural bacterial communities by PCR-based techniques. Minerva Biotecnol. 1996, 8:126-134.
11. Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
12. Fialová J., Chumchalová J., Miková K., Hrusová I. Effect of food preservatives on the growth of spilage lactobacilli isolated from mayonnaise-based sauces. Food Control 2008, 19:706-713.
13. Gallina S., Bianchi D.M., Ru G., Maurella C., Barzanti P., Baioni E., Virgilio S., Mioni R., Lanni L., Migliazzo A. Microbiological recovery from bovine, swine, equine, and ovine carcasses: comparison of excision, sponge and swab sampling methods. Food Control 2014, 50:919-924.
14. Gihring T.M., Green S.J., Schadt C.W. Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ. Microbiol. 2012, 14:285-290.
15. Harper B.A., Barbut S., Lim L.T., Marcone M.F. Microstructural and textural investigation of various manufactured collagen sausage casings. Food Res. Int. 2012, 49:494-500.
16. Heinz G., Hautzinger P. Meat processing technology for small to medium scale producers. Casings 2007, RAP Publication (FAO).
17. Janczyk P., Pieper R., Smidt H., Souffrant W.B. Changes in the diversity of pig ileal lactobacilli around weaning determined by means of 16S rRNA gene amplification and denaturing gradient gel electrophoresis. FEMS Microbiol. Ecol. 2007, 61:132-140.
18. Kozačinski L., Drosinos E., Čaklovica F., Cocolin L., Gasparik-Reichardt J., Vesković S. Investigation of microbial association of traditionally fermented sausages. Food Technol. Biotechnol. 2008, 46:93-106.
19. Leroy S., Giammarinaro P., Chacornac J.-P., Lebert I., Talon R. Biodiversity of indigenous staphylococci of naturally fermented dry sausages and manufacturing environments of small-scale processing units. Food Microbiol. 2010, 27:294-301.
20. Lundin D., Severin I., Logue J.B., Östman Ö., Andersson A.F., Lindström E.S. Which sequencing depth is sufficient to describe patterns in bacterial α-and β-diversity?. Environ. Microbiol. Rep. 2012, 4:367-372.
21. Masella A.P., Bartram A.K., Truszkowski J.M., Brown D.G., Neufeld J.D. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinf. 2012, 13:31.
22. McDonald D., Price M.N., Goodrich J., Nawrocki E.P., DeSantis T.Z., Probst A., Andersen G.L., Knight R., Hugenholtz P. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2011, 6:610-618.
23. Moreau M.M., Eades S.C., Reinemeyer C.R., Fugaro M.N., Onishi J.C. Illumina sequencing of the V4 hypervariable region 16S rRNA gene reveals extensive changes in bacterial communities in the cecum following carbohydrate oral infusion and development of early-stage acute laminitis in the horse. Vet. Microbiol. 2014, 168:436-441.
24. Nakyinsige K., Man Y.B.C., Sazili A.Q. Halal authenticity issues in meat and meat products. Meat Sci. 2012, 91:207-214.
25. Paulson J.N., Pop M., Bravo H.C. Metastats: an improved statistical method for analysis of metagenomic data. Genome Biol. 2011, 12:1-27.
26. Połka J., Rebecchi A., Pisacane V., Morelli L., Puglisi E. Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons. Food Microbiol. 2015, 46:342-356.
27. Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., Glöckner F.O. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007, 35:7188-7196.
28. Rahimi E., Jalali M., Weese J.S. Prevalence of Clostridium difficile in raw beef, cow, sheep, goat, camel and buffalo meat in Iran. BMC Public Health 2014, 14:119.
29. Rantsiou K., Iacumin L., Cantoni C., Comi G., Cocolin L. Ecology and characterization by molecular methods of Staphylococcus species isolated from fresh sausages. Int. J. Food Microbiol. 2005, 97:277-284.
30. R Development Core Team A Language and Environment for Statistical Computing 2012, R Foundation for Statistical Computing, Vienna, Austria.
31. Rebecchi A., Crivori S., Sarra P.G., Cocconcelli P.S. Physiological and molecular techniques for the study of bacterial community development in sausage fermentation. J. Appl. Microbiol. 1998, 84:1043-1049.
32. Schloss P.D. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput. Biol. 2010, 6:e1000844.
33. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
34. Vasileiadis S., Puglisi E., Arena M., Cappa F., Veen J.A., Cocconcelli P.S., Trevisan M. Soil microbial diversity patterns of a lowland spring environment. FEMS Microbiol. Ecol. 2013, 86:172-184.
35. Vauterin L., Vauterin P. Computer-aided objective comparison of electrophoresis patterns for grouping and identification of microorganisms. Eur. Microbiol. 1992, 1:37-41.
36. Versalovic J., Schneider M., De Bruijn F.J., Lupski J.R. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 1994, 5:25-40.
37. Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naive Bayesian Classifier for rapid assignment of rRNA sequences into the New Bacterial Taxonomy. Appl. Environ. Microbiol. 2007, 73:5261-5267.
38. Wu Y.-C., Chi S.-P. Casings. Handbook of Fermented Meat and Poultry 2010, 101-110. Blackwell publishing, Ames, Iowa, USA. F. Toldrà (Ed.).