Cherie J. Ziemer

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall α-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast α-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the microbiota. Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of α-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes. Co-culturing studies showed that metabolism of yeast mannan by B. thetaiotaomicron presents a ‘selfish’ model for the catabolism of this difficult to breakdown polysaccharide. Genomic comparison with B. thetaiotaomicron in conjunction with cell culture studies show that a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet.

Fate and transport of zoonotic, bacterial, viral, and parasitic pathogens during swine manure treatment, storage, and land application

Members of the public are always somewhat aware of foodborne and other zoonotic pathogens; however, recent illnesses traced to produce and the emergence of pandemic H1N1 influenza virus have increased the scrutiny on all areas of food production. The Council for Agricultural Science and Technology has recently published a comprehensive review of the fate and transport of zoonotic pathogens that can be associated with swine manure. The majority of microbes in swine manure are not zoonotic, but several bacterial, viral, and parasitic pathogens have been detected. Awareness of the potential zoonotic pathogens in swine manure and how treatment, storage, and handling affect their survival and their potential to persist in the environment is critical to ensure that producers and consumers are not at risk. This review discusses the primary zoonotic pathogens associated with swine manure, including bacteria, viruses, and parasites, as well as their fate and transport. Because the ecology of microbes in swine waste is still poorly described, several recommendations for future research are made to better understand and reduce human health risks. These recommendations include examination of environmental and ecological conditions that contribute to off-farm transport and development of quantitative risk assessments.

Swine odor analyzed by odor panels and chemical techniques.

The National Research Council identified odors as a significant animal emission and highlighted the need to develop standardized protocols for sampling and analysis. The purpose of our study was to compare different odor sampling techniques for monitoring odors emitted from stored swine manure. In our study, odorous headspace air from swine manure holding tanks were analyzed by human panels and analytical techniques. Odorous air was analyzed by human panels using dynamic dilution olfactometry (DDO). Chemical analysis used acid traps for ammonia (NH₃), fluorescence for hydrogen sulfide (H₂S), and thermal desorption gas chromatography-mass spectrometry for volatile organic compounds (VOCs). Chemical analysis included the use of gas chromatography-olfactometry (GC-O) for determining key odorants. Chemical odorant concentrations were converted to odor activity values (OAVs) based on literature odor thresholds. The GC-O technique used was GC-SNIF. Dilution thresholds measured by different odor panels were significantly different by almost an order of magnitude even though the main odorous compound concentrations had not changed significantly. Only 5% of the key odorous VOCs total OAVs was recovered from the Tedlar bags used in DDO analysis. Ammonia was the only chemical odorant significantly correlated with DDO analysis in the fresh (1 wk) and aged manure. Chemical analysis showed that odor concentration stabilized after 5 to 7 wk and that HS was the most dominant odorant. In aged manure, neither volatile fatty acids (VFAs) nor HS was correlated with any other chemical odorant, but NH, phenols, and indoles were correlated, and phenols and indoles were highly correlated. Correlation of odorant concentration was closely associated with the origin of the odorant in the diet. Key odorants determined by chemical and GC-O included indoles, phenols, NH₃, and several VFAs (butanoic, 3-methylbutanoic, and pentanoic acids).

Comparative sulfur analysis using thermal combustion or inductively coupled plasma methodology and mineral composition of common livestock feedstuffs

The objective of this study was to compare the use of thermal combustion (CNS) and inductively coupled plasma (ICP) to measure the total S content in plant-, animal-, and mineral-based feedstuffs, and to provide concentrations of other macro- and micro-minerals contained in these feedstuffs. Forty-five feedstuffs (464 total samples) were obtained from suppliers as well as swine feed and pet food manufacturers throughout the United States. Mineral data from IPC analysis were summarized on a DM basis using sample mean and SD, whereas the comparison of total S content between CNS and ICP was examined by bivariate plot and correspondence correlation. Analyses of a wide range of feedstuffs by CNS and ICP for total S were comparable for all but a few feedstuffs. For potassium iodide and tribasic copper chloride, ICP estimated total S to be lower than when analyzed by CNS (bias = 2.51 +/- 0.15 SE, P < 0.01). In contrast, for defluorinated phosphate and limestone, ICP estimated total S to be greater than when analyzed by CNS (bias = -1.46 +/- 0.51 SE, P < 0.01). All other samples had similar estimates of total S, whether analyzed by CNS or ICP. As expected, S composition varied greatly among feedstuffs. For total S, plant-based feedstuffs generally had lower total S compared with animal-based feedstuffs, whereas minerals supplied in sulfate form had the greatest concentration of total S. In addition to total S, mineral composition data are provided for all feedstuffs as obtained by ICP analysis. Within specific feedstuffs, mineral composition was quite variable, potentially due to low concentrations in the feed-stuff causing high mathematical variation or due to the source of feedstock obtained. In general, analyzed values of P were similar to previous tabular values. These data provide feed formulators a database from which modifications in dietary minerals can be accomplished and from which mineral requirements can be met more precisely to reduce losses of minerals into the environment.

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen.

Corrigendum: Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

This corrects the article DOI: 10.1038/nature13995

Dysbiosis Characterized by Reduced Abundance of Roseburia is Associated With Increased Severity of Colitis in IL-10−/− Mice

G A A b st ra ct s estimated by real-time PCR assay using oligonucleotide primers specific to immediate early gene. More than 10 copies/μg DNA of PCR amplicons were defined as positive. We compared the positive ratio of those colonoscopic findings of UC patients between positive and negative for CMV-DNA. Additionally, we examined the correlation between the number of CMVDNA amplicons [negative, low-copy group (10-100 copies/μg DNA), high-copy group (≧100 copies/μg DNA)], and colonoscopic features and their medications. Results: Positive ratio of ulcerative lesions was higher in CMV-DNA-positive group than in CMV-DNA-negative group [22/34 (64.7%) vs. 10/27 (37.0%), p<0.05]. Further analysis in limited to UC patients who had no ulcerative lesions revealed that the positive ratio of edema or redness in CMVDNA-positive groupwere significantly higher than in CMV-DNA-negative UC group [redness, 8/12 (66.7%) vs. 4/17 (23.5%); edema, 7/12 (58.3%) vs. 2/17 (11.8%)]. Moreover, the positive ratio of edema or redness is higher even in low-copy group of CMV-DNA-positive UC patients (Table). Ratio of UC patients treated with the combination of steroids and immunomodulators is significantly higher in the high-copy group than in other groups [negative, 3/27 (11.1%); low-copy group, 1/10 (10.0%); high-copy group, 11/24 (45.8%)]. Conclusions: In addition to ulcerative lesions, reddish and edematous colonic mucosa might be characteristic of early colonoscopic features in UC patients concomitant with CMV reactivation. CMV reactivation can be easily occurred in patients with UC refractory to the combined therapies of steroids and immunomodulators.

Improved Hybrid Genome Assemblies of Two Strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, Obtained Using Illumina and 454 Sequencing Technologies

ABSTRACT Bacteroides xlyanisolvens strains (SD_CC_1b, SD_CC_2a) isolated from human feces were grown on crystalline cellulose. Cellulolytic properties are not common in Bacteroides species. Here, we report improved genome sequences of both of the B. xlyanisolvens strains.