Characterization of the Biodiversity of the Spoilage Microbiota in Chicken Meat Using Next Generation Sequencing and Culture Dependent Approach

Abstract

This study investigated the psychrotrophic bacteria isolated from chicken meat to characterize their microbial composition during refrigerated storage. The bacterial community was identified by the Illumina MiSeq method based on bacterial DNA extracted from spoiled chicken meat. Molecular identification of the isolated psychrotrophic bacteria was carried out using 16S rDNA sequencing and their putrefactive potential was investigated by the growth at low temperature as well as their proteolytic activities in chicken meat. From the Illumina sequencing, a total of 187,671 reads were obtained from 12 chicken samples. Regardless of the type of chicken meat (i.e., whole meat and chicken breast) and storage temperatures (4°C and 10°C), Pseudomonas weihenstephanensis and Pseudomonas congelans were the most prominent bacterial species. Serratia spp. and Acinetobacter spp. were prominent in chicken breast and whole chicken meat, respectively. The 118 isolated strains of psychrotrophic bacteria comprised Pseudomonas spp. (58.48%), Serratia spp. (10.17%), and Morganella spp. (6.78%). All isolates grew well at 10°C and they induced different proteolytic activities depending on the species and strains. Parallel analysis of the next generation sequencing and culture dependent approach provides in-depth information on the biodiversity of the spoilage microbiota in chicken meat. Further study is needed to develop better preservation methods against these spoilage bacteria.

Diversity and anaerobic growth ofPseudomonasspp. isolated from modified atmosphere packaged minced beef

“…; Lee et al . ) with reported lipolytic and proteinolytic activity (Stead ; Alquati et al . ; Marchand et al .…”

“…The dominant Pseudomonas species detected in this study were identified as P. weihenstephanensis, P. fragi and P. lundensis. These species have been described as potential meat spoilers as well as raw milk spoilers (Shaw and Latty 1982;Labadie 1999;Ercolini et al 2007;Von Neubeck et al 2016;Lee et al 2017) with reported lipolytic and proteinolytic activity (Stead 1986;Alquati et al 2002;Marchand et al 2009;Stoeckel et al 2016). Additionally, isolates could be affiliated to P. versuta, P. meridiana, P. simiae and P. veronii.…”

The occurrence of Salmonella, extended‐spectrum β‐lactamase producing Escherichia coli and carbapenem resistant non‐fermenting Gram‐negative bacteria in a backyard poultry flock environment

“…Moreover, Acinetobacter spp. are also associated with chicken meat spoilage (Barnes & Impey, 1968;Lee et al, 2017;Nychas et al, 2008;Russell, Fletcher, & Cox, 1996;Zhang et al, 2012). Thus, it is likely that Acinetobacter spp.…”

“…are naturally found in live poultry, poultry environment and/or poultry products (Arnaut-Rollier, De Zutter, & Van Hoof, 1999;Ayres & Walker, 1956;Bergeron et al, 2012;van den Bogaard, London, Driessen, & Stobberingh, 2001;Booth & Arnold, 2003;Ellerbroek, 1997;Glendinning, McLachlan, & Vervelde, 2017;Hatew, Delessa, Zakin, & Gollop, 2011;Leahy, 2015;Lee, Kwon, Heo, Kim, & Kim, 2017;Mayes & Takeballi, 1983;Mead & Adams, 1977;Shabbir et al, 2015;Sundheim, Sletten, & Dainty, 1998;Vadehra, Baker, & Naylor, 1970;Zhang et al, 2012). Moreover, the transmission of E. coli and other non-fermenting GNB such as Acinetobacter spp., and Pseudomonas spp from live birds or their products to people has been tangentially reported in the literature (Leahy, 2015;van den Bogaard et al, 2001).…”

Misannotations of the genes encoding sugar N‐formyltransferases

“…In terms of biological relevance, P. congelans , first isolated in Germany and possibly phytopathogenic, is a Gram‐negative fluorescent bacterium associated with the phyllosphere of grasses . It has also been shown recently to be a prominent species in spoiled chicken meat . Shewanella species are Gram‐negative bacteria that inhabit marine environments and that may play a role in human disease.…”