Persistence of Escherichia coli O157:H7 and Total Escherichia coli in Feces and Feedlot Surface Manure from Cattle Fed Diets with and without Corn or Sorghum Wet Distillers Grains with Solubles

- Invited Review - Assessment of the gastrointestinal microbiota using 16S ribosomal RNA gene amplicon sequencing in ruminant nutrition

The gastrointestinal (GI) tract of ruminants contains diverse microbes that ferment various feeds ingested by animals to produce various fermentation products, such as volatile fatty acids. Fermentation products can affect animal performance, health, and well-being. Within the GI microbes, the ruminal microbes are highly diverse, greatly contribute to fermentation, and are the most important in ruminant nutrition. Although traditional cultivation methods provided knowledge of the metabolism of GI microbes, most of the GI microbes could not be cultured on standard culture media. By contrast, amplicon sequencing of 16S rRNA genes can be used to detect unculturable microbes. Using this approach, ruminant nutritionists and microbiologists have conducted a plethora of nutritional studies, many including dietary interventions, to improve fermentation efficiency and nutrient utilization, which has greatly expanded knowledge of the GI microbiota. This review addresses the GI content sampling method, 16S rRNA gene amplicon sequencing, and bioinformatics analysis and then discusses recent studies on the various factors, such as diet, breed, gender, animal performance, and heat stress, that influence the GI microbiota and thereby ruminant nutrition.

Circulation of Shiga Toxin-Producing Escherichia coli Phylogenetic Group B1 Strains Between Calve Stable Manure and Pasture Land With Grazing Heifers

Escherichia coli strains carrying Shiga toxins 1 and 2 (stx₁ and stx₂), intimin (eae), and hemolysin (ehxA) production genes were found in grass shoot, rhizosphere soil, and stable manure samples from a small-scale cattle farm located at the center of Netherlands, using cultivation-dependent and -independent microbiological detection techniques. Pasture land with grazing heifers in the first year of sampling in 2014 and without grazing cattle in 2015 was physically separated from the stable that housed rose calves during both years. Manure from the stable was applied to pasture via injection into soil once per year in early spring. Among a variety of 35 phylogenetic distinctly related E. coli strains, one large group consisting of 21 closely resembling E. coli O150:H2 (18), O98:H21 (2), and O84:H2 (1) strains, all belonging to phylogenetic group B1 and carrying all screened virulence traits, was found present on grass shoots (10), rhizosphere soil (3), and stable manure (8) in 2014, but not anymore in 2015 when grazing heifers were absent. Presence and absence of these strains, obtained via enrichments, were confirmed via molecular detection using PCR-NALFIA in all ecosystems in both years. We propose that this group of Shiga toxin-producing E. coli phylogenetic group B1 strains was originally introduced via stable manure injection into the pasture. Upon grazing, these potential pathogens proliferated in the intestinal track systems of the heifers resulting in defecation with higher loads of the STEC strain onto the grass cover. The STEC strain was further smeared over the field via the hooves of the heifers resulting in augmentation of the potential pathogen in the pasture in 2014, whereas in 2015, in the absence of heifers, no augmentation occurred and only a more diverse group of potentially mild virulent E. coli phylogenetic group A and B1 strains, indigenous to pasture plants, remained present. Via this model, it was postulated that human pathogens can circulate between plants and farm animals, using the plant as an alternative ecosystem. These data indicate that grazed pasture must be considered as a potential carrier of human pathogenic E. coli strains and possibly also of other pathogens.

High resolution characterisation of E. coli proliferation profiles in livestock faeces

Agricultural intensification can lead to high volumes of livestock faeces being applied to land, either as solid or liquid manures or via direct defecation, and can result in reservoirs of faecal indicator organisms (FIOs) persisting within farmland. Understanding the survival of FIOs, e.g. E. coli, in agricultural environments, and in particular within different livestock faeces, is key to developing catchment management practices for the protection of ecosystem services provided by clean water. Frequently, controlled laboratory studies, under constant temperature regimes, are used to determine the impact of environmental factors on E. coli persistence in livestock faeces; however, such studies oversimplify the diurnal variations and interactions of real world conditions. The aim of this study was to investigate the survival of E. coli using a controlled environment facility, which simulated diurnal variation of temperatures typically experienced during a British spring and summer. The approach provided a comparison of E. coli persistence profiles within faeces of sheep, beef cattle and dairy cattle to allow novel interpretations of E. coli regrowth patterns in contrasting livestock faeces in the period immediately post-defecation. Thus, the coupling of a tightly controlled environment facility with high resolution monitoring enabled the development of a new non-linear, asymptotic description of E. coli proliferation in livestock faeces, with increased potential for E. coli growth observed during warmer temperatures for all livestock types. While this study focused on temperatures typical of the UK, the occurrence of a phase of E. coli regrowth has implications for microbial water quality management worldwide.