The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

Fouhy, Fiona; Deane, Jennifer; Rea, Mary C.; O’Sullivan, Órla; Ross, R. Paul; O'Callaghan, G.; Plant, Barry J.; Stanton, Catherine

doi:10.1371/journal.pone.0119355

Cited by 243 publications

(207 citation statements)

References 27 publications

Supporting

Mentioning

182

Contrasting

Unclassified

Order By: Relevance

“…Distances below 0.05 were not shown extraction yield and the proportions of some genera observed among bacterial communities observed on SWM (Metzler-Zebeli et al 2016). However, it was demonstrated that freezing may only have minor impacts on the global portrait of a bacterial community (Fouhy et al 2015), on which this study focused. The short read lengths (400-440 bp) enabled a thorough taxonomic assignment for all samples at the genus level, with an overall low abundance of 1% of unclassified phyla.…”

Section: Discussionmentioning

confidence: 68%

A sequencing approach targeting the 16S rRNA gene unravels the biofilm composition of spiral-wound membranes used in the dairy industry

Chamberland

Lessard

Doyen

et al. 2016

Dairy Sci. & Technol.

View full text Add to dashboard Cite

Few data are available concerning the composition of biofilms found at the surface of filtration membranes, which, to some extent, explains the long-term failure of numerous strategies developed to control biofouling. This preliminary study intended to design a metagenomic tool targeting the 16S rRNA gene in order to unravel a general portrait of bacterial communities found on spiral-wound membranes used in the dairy industry. A total of seven spiral-wound membrane elements (ultrafiltration, nanofiltration, or reverse osmosis) at the end of their useful lifetimes were collected from different dairy plants. Targeted analysis of the 16S rRNA genes of the metagenome extracted from the membranes revealed their bacterial diversity via high-throughput sequencing technology (Miseq, Illumina). It was found that the nature of the filtered fluid (milk, whey, water) explained 58.6 % of the variance observed between communities found on membranes. Treatments applied on dairy fluids (milk pasteurization, whey bleaching or whey ultrafiltration) induced a selective pressure that affected the diversity of bacterial communities found on membranes and the proportions of spore-former bacteria among them. This work provides the first complete bacterial portrait of the biofilm composition of spiral-wound membranes used in the dairy industry. It suggests that the nature of the filtered fluid and potentially filtration Dairy Sci. & Technol. (2017)

show abstract

Section: Discussionmentioning

confidence: 68%

A sequencing approach targeting the 16S rRNA gene unravels the biofilm composition of spiral-wound membranes used in the dairy industry

Chamberland

Lessard

Doyen

et al. 2016

Dairy Sci. & Technol.

View full text Add to dashboard Cite

show abstract

“…PCRs were completed on the template DNA. Initially, the DNA was amplified with primers specific to the V3-V4 region of the 16S rRNA gene which also incorporates the Illumina overhang adaptor (forward primer, 5=-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG; reverse primer, 5=-GTCTCGT GGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC) (36). Each PCR mixture contained DNA template (ca.…”

Section: Methodsmentioning

confidence: 99%

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

Doyle

Gleeson

O’Toole

et al. 2017

Appl Environ Microbiol

132

121

View full text Add to dashboard Cite

In pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. High-throughput sequencing on a variety of microbial niches on farms was used to study the patterns of microbial movement through the dairy production chain and, in the process, to investigate the impact of seasonal housing and the inclusion/exclusion of a teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor. Beta diversity and network analyses showed that environmental and milk microbiotas separated depending on whether they were sourced from an indoor or outdoor environment. Within these respective habitats, similarities between the milk microbiota and that of teat swab samples and, to a lesser extent, fecal samples were apparent. Indeed, SourceTracker identified the teat surface as the most significant source of contamination, with herd feces being the next most prevalent source of contamination. In milk from cows grazing outdoors, teat prep significantly increased the numbers of total bacteria present. In summary, sequence-based microbiota analysis identified possible sources of raw milk contamination and highlighted the influence of environment and farm management practices on the raw milk microbiota. IMPORTANCEThe composition of the raw milk microbiota is an important consideration from both a spoilage perspective and a food safety perspective and has implications for milk targeted for direct consumption and for downstream processing. Factors that influence contamination have been examined previously, primarily through the use of culture-based techniques. We describe here the extensive application of high-throughput DNA sequencing technologies to study the relationship between the milk production environment and the raw milk microbiota. The results show that the environment in which the herd was kept was the primary driver of the composition of the milk microbiota composition.KEYWORDS farm practices, food chain, food safety, metagenomics, microbial source tracking, raw milk microbiota T he impact of the dairy farm environment on the microbial composition of raw milk and raw milk products has been appreciated for some time (1). There are numerous niches that collectively constitute the dairy farm environment, and these harbor a vast array of microbes. The transfer of microbes from the farm environment to raw milk can be influenced be a number of factors, including farmer hygiene, husbandry practices,

show abstract

“…Microbial profiling was performed using high-throughput sequencing of the V3-V4 region of the 16S rRNA gene (paired-end reads of 300 bp or 250 bp) on an Illumina MiSeq platform according to the standard Illumina protocol, except that the PCR mix volume was doubled in the first PCR step, and 30 cycles were used instead of 25 (66). Any samples with less than 40,000 postquality reads were removed from the analysis.…”

Section: Figmentioning

confidence: 99%

Exploring a Possible Link between the Intestinal Microbiota and Feed Efficiency in Pigs

McCormack

Curião

Buzoianu

et al. 2017

Appl Environ Microbiol

260

208

View full text Add to dashboard Cite

Feed efficiency (FE) is critical in pig production for both economic and environmental reasons. As the intestinal microbiota plays an important role in energy harvest, it is likely to influence FE. Therefore, our aim was to characterize the intestinal microbiota of pigs ranked as low, medium, and high residual feed intake ([RFI] a metric for FE), where genetic, nutritional, and management effects were minimized, to explore a possible link between the intestinal microbiota and FE. Eightyone pigs were ranked according to RFI between weaning and day 126 postweaning, and 32 were selected as the extremes in RFI (12 low, 10 medium, and 10 high). Intestinal microbiota diversity, composition, and predicted functionality were assessed by 16S rRNA gene sequencing. Although no differences in microbial diversity were found, some RFI-associated compositional differences were revealed, principally among members of Firmicutes, predominantly in feces at slaughter (albeit mainly for low-abundance taxa). In particular, microbes associated with a leaner and healthier host (e.g., Christensenellaceae, Oscillibacter, and Cellulosilyticum) were enriched in low RFI (more feed-efficient) pigs. Differences were also observed in the ileum of low RFI pigs; most notably, Nocardiaceae (Rhodococcus) were less abundant. Predictive functional analysis suggested improved metabolic capabilities in these animals, especially within the ileal microbiota. Higher ileal isobutyric acid concentrations were also found in low RFI pigs. Overall, the differences observed within the intestinal microbiota of low RFI pigs compared with that of their high RFI counterparts, albeit relatively subtle, suggest a possible link between the intestinal microbiota and FE in pigs.IMPORTANCE This study is one of the first to show that differences in intestinal microbiota composition, albeit subtle, may partly explain improved feed efficiency (FE) in low residual feed intake (RFI) pigs. One of the main findings is that, although microbial diversity did not differ among animals of varying FE, specific intestinal microbes could potentially be linked with porcine FE. However, as the factors impacting FE are still not fully understood, intestinal microbiota composition may not be a major factor determining differences in FE. Nonetheless, this work has provided a potential set of microbial biomarkers for FE in pigs. Although culturability could be a limiting factor and intervention studies are required, these taxa could potentially be targeted in the future to manipulate the intestinal microbiome so as to improve

show abstract

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

Cited by 243 publications

References 27 publications

A sequencing approach targeting the 16S rRNA gene unravels the biofilm composition of spiral-wound membranes used in the dairy industry

A sequencing approach targeting the 16S rRNA gene unravels the biofilm composition of spiral-wound membranes used in the dairy industry

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

Exploring a Possible Link between the Intestinal Microbiota and Feed Efficiency in Pigs

Contact Info

Product

Resources

About