Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H2), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H2 metabolism. Two-thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyse H2 production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g., Ruminococcus) accounted for half of all hydrogenase transcripts. Various H2 uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate and nitrite reduction (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis-related transcripts predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared with pure culture. We conclude that H2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognised. There is evidence that alternative hydrogenotrophs, including acetogenic and respiratory bacteria, can prosper in the rumen and effectively compete with methanogens for H2. These findings may help to inform ongoing strategies to mitigate methane emissions by increasing flux through alternative H2 uptake pathways, including through animal selection, dietary supplementation and methanogenesis inhibitors.

Nitrogen metabolism in gut systems remains poorly studied in spite of its importance for microbial growth and its implications for the metabolism of the host. Prevotella spp. are the most predominant bacteria detected in the rumen, but their presence has also been related to health and disease states in the human gut and oral cavity. To explore the metabolic networks for nitrogen assimilation in this bacterium, changes in gene expression profiles in response to variations in the available nitrogen source and to different concentrations of ammonium were analyzed by microarray and reverse transcription quantitative PCR, and linked with function by further proteomic analysis. The observed patterns of transcript abundances for genes involved in ammonium assimilation differed from the classical “enteric paradigm” for nitrogen utilization. Expression of genes encoding high substrate affinity nitrogen assimilation enzymes (GS-GOGAT system) was similar in growth-limiting and non-limiting nitrogen concentrations in P. ruminicola 23, whereas E. coli and Salmonella spp. responses to excess nitrogen involve only low substrate affinity enzymes. This versatile behavior might be a key feature for ecological success in habitats such as the rumen and human colon where nitrogen is rarely limiting for growth, and might be linked to previously reported Prevotella spp. population imbalances relative to other bacterial species in gut systems.

Potentially hazardous foods require time/temperature control for safety. According to the U.S. Food and Drug Administration Food Code, most cheeses are potentially hazardous foods based on pH and water activity, and a product assessment is required to evaluate safety of storage >6 h at 21°C. We tested the ability of 67 market cheeses to support growth of Listeria monocytogenes (LM), Salmonella spp. (SALM), Escherichia coli O157:H7 (EC), and Staphylococcus aureus (SA) over 15 days at 25°C. Hard (Asiago and Cheddar), semi-hard (Colby and Havarti), and soft cheeses (mozzarella and Mexican-style), and reduced-sodium or reduced-fat types were tested. Single-pathogen cocktails were prepared and individually inoculated onto cheese slices (∼10(5) CFU/g). Cocktails were 10 strains of L. monocytogenes, 6 of Salmonella spp., or 5 of E. coli O157:H7 or S. aureus. Inoculated slices were vacuum packaged and stored at 25°C for ≤ 15 days, with surviving inocula enumerated every 3 days. Percent salt-in-the-moisture phase, percent titratable acidity, pH, water activity, and levels of indigenous/starter bacteria were measured. Pathogens did not grow on 53 cheeses, while 14 cheeses supported growth of SA, 6 of SALM, 4 of LM, and 3 of EC. Of the cheeses supporting pathogen growth, all supported growth of SA, ranging from 0.57 to 3.08 log CFU/g (average 1.70 log CFU/g). Growth of SALM, LM, and EC ranged from 1.01 to 3.02 log CFU/g (average 2.05 log CFU/g), 0.60 to 2.68 log CFU/g (average 1.60 log CFU/g), and 0.41 to 2.90 log CFU/g (average 1.69 log CFU/g), respectively. Pathogen growth varied within cheese types or lots. Pathogen growth was influenced by pH and percent salt-in-the-moisture phase, and these two factors were used to establish growth/no-growth boundary conditions for safe, extended storage (≤25°C) of pasteurized milk cheeses. Pathogen growth/no-growth could not be predicted for Swiss-style cheeses, mold-ripened or bacterial surface-ripened cheeses, and cheeses made with nonbovine milk, as insufficient data were gathered. This challenge study data can support science-based decision making in a regulatory framework.

Clostridium perfringens is an opportunistic pathogenic bacterium that infects both animals and humans. Clostridium perfringens genomes encode a diverse array of toxins and virulence proteins, which continues to expand as more genomes are sequenced. In this study, the genomes of 44 C. perfringens strains isolated from intestinal sections of diseased cattle and from broiler chickens from diseased and healthy flocks were sequenced. These newly assembled genomes were compared to 141 publicly available C. perfringens genome assemblies, by aligning known toxin and virulence protein sequences in the assemblies using BLASTp. The genes for alpha toxin, collagenase, a sialidase (nanH), and alpha-clostripain were present in at least 99% of assemblies analyzed. In contrast, beta toxin, epsilon toxin, iota toxin, and binary enterotoxin of toxinotypes B, C, D, and E were present in less than 5% of assemblies analyzed. Additional sequence variants of beta2 toxin were detected, some of which were missing the leader or signal peptide sequences and therefore likely not secreted. Some pore-forming toxins involved in intestinal diseases were host-associated, the netB gene was only found in avian isolates, while netE, netF, and netG were only present in canine and equine isolates. Alveolysin was positively associated with canine and equine strains and only present in a single monophyletic clade. Strains from ruminant were not associated with known virulence factors and, except for the food poisoning associated clade, were present across the phylogenetic diversity identified to date for C. perfringens. Many C. perfringens strains associated with food poisoning lacked the genes for hyaluronidases and sialidases, important for attaching to and digesting complex carbohydrates found in animal tissues. Overall, the diversity of virulence factors in C. perfringens makes these species capable of causing disease in a wide variety of hosts and niches.

The non-O157 Shiga toxigenic Escherichia coli (STEC) serogroups most commonly associated with illness are O26, O45, O103, O111, O121, and O145. We compared the thermal tolerance (D55°C) of three or more strains of each of these six non-O157 STEC serogroups with five strains of O157:H7 STEC in 7% fat ground beef. D55°C was also determined for at least one heat-tolerant STEC strain per serogroup in 15 and 27% fat ground beef. D55°C of single-pathogen cocktails of O157 and non-O157 STEC, Salmonella, and potential pathogen surrogates, Pediococcus acidilactici and Staphylococcus carnosus, was determined in 7, 15, and 27% fat ground beef and in frankfurter batter. Samples (25 g) were heated for up to 120 min at 55°C, survivors were enumerated, and log CFU per gram was plotted versus time. There were significant differences in D55°C across all STEC strains heated in 7% fat ground beef (P < 0.05), but no non-O157 STEC strain had D55°C greater than the range observed for O157 STEC. D55°C was significantly different for strains within serogroups O45, O145, and O157 (P < 0.05). D55°C for non-O157 STEC strains in 15 and 27% fat ground beef were less than or equal to the range of D55°C for O157. D55°C for pathogen cocktails was not significantly different when measured in 7, 15, and 27% fat ground beef (P ≥ 0.05). D55°C of Salmonella in frankfurter batter was significantly less than for O157 and non-O157 STEC (P < 0.05). Thermal tolerance of pathogen cocktails in ground beef (7, 15, or 27% fat) and frankfurter batter was significantly less than for potential pathogen surrogates (P < 0.05). Results suggest that thermal processes in beef validated against E. coli O157:H7 have adequate lethality against non-O157 STEC, that thermal processes that target Salmonella destruction may not be adequate against STEC in some situations, and that the use of pathogen surrogates P. acidilactici and S. carnosus to validate thermal processing interventions in ground beef and frankfurter batter would be of limited utility to processors.