Evaluation of culture methods for investigation of Salmonella enterica serovar ecology in feces

The present study evaluated culture methods to optimize detection and isolation of a wide range of Salmonella serovars. Fecal samples were obtained from cows, horses and pigs. Select samples were seeded with antibiotic resistance carrying S. Typhimurium and S. Choleraesuis as positive controls

Abattoir holding pens as a source of Salmonella for swine.

This study was designed to determine if rapid Salmonella infection is possible during the pre-slaughter holding period at swine abattoirs. For 24 groups of pigs studied in 2 high capacity abattoirs, pooled fecal samples were collected from the transport trailer right after pigs were unloaded (pre-holding samples). Holding pens were sampled prior to the entry of study pigs for the pre-slaughter holding. After slaughter, cecal contents and ileocecal lymph nodes were collected from 30 pigs in each studied group (post-holding samples). From all holding pens sampled (100%) at least one Salmonella serovar was isolated. All groups of pigs were Sa/monel/a-positive in the post-holding sampling, including those groups Salmonella-negative in the pre-holding sampling. Some groups had Salmonella serovars that matched serovars isolated from the holding pens, but not with serovars isolated from the pre-holding samples. Results indicate that the abattoir holding pens constitute an important source of Salmonella infections for swine

Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria

Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central for defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/Bacteroides xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multilocus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors

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.publishersversionPeer reviewe

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

Evaluation of culture methods for investigation of Salmonella enterica serovar ecology in feces

The present study evaluated culture methods to optimize detection and isolation of a wide range of Salmonella serovars. Fecal samples were obtained from cows, horses and pigs. Select samples were seeded with antibiotic resistance carrying S. Typhimurium and S. Choleraesuis as positive controls.</p

Identification of enzymatic processes for the breakdown of crystalline cellulose

Issued as final reportLignin, cellulose and hemicellulose, the key components of lignocellulosic biomass are closely associated with each other at the plant cell level. This close association, together with the partly crystalline nature of cellulose serves to protect cellulose in native biomass from enzymatic hydrolysis. The predominant polysaccharide in most plant cell walls is cellulose, which forms long liner fibrils of approximately 30-40 hydrogen-bonded chains of β-(1,4) glucopyranosides that have a native degree of polymerization (DP) of ~2,000-15,000 depending the starting bioresource (O’Sullivan, 1997). Cellulose can exhibit several different supra-molecular structures, including amorphous, para-crystalline and crystalline. Native cellulose has been shown to be composed of two different crystalline forms in addition to para-crystalline and amorphous (Attala, et al., 1984). In general, the bioavailability of cellulose is controlled by a variety of factors including the degree of cellulose crystallinity, lignin content and structure, acetylated hemicelluloses and lignin-carbohydrate complexes (Clark, A.J., 1997). The deconstruction of cellulose to glucose has become a key technological challenge for green biofuel production. Researchers are searching for novel cellulolytic enzymatic properties in many organisms including termites, sea worms, and the gut section of several mammalians (Baker, J.O., et al., 1998; Mansfield, S.D., et al., 2003; McCarter, S.L., et al., 2002; Wyman, C.E., 2005). The crystalline regions of cellulose are normally considered to be more difficult to degrade than amorphous domains due to chains tightly-held by intermolecular hydrogen bonding. Several researchers demonstrated increased crystallinity during enzymatic hydrolysis, and concluded that the loosely structured amorphous regions were hydrolyzed more rapid than the crystalline domains (Cao, Y., et al., 2002; Cao, Y., et al. 2004). The intestinal Fortitude Fibro-biotic program did find two bacterial isolates that had a unique enzyme activity on cellulose resulting in treated cellulose samples having a decrease in crystallinity. This type of enzymatic activity has not been previously reported or isolated for biofuel production. Two bacterial isolates (SDCC 1b and SDCC 2a) have had their genomes sequenced and are in the process of genome annotation. This research program was directed at determining how cellulosic ultrastructure changes when fermented with these novel mammalian bacterial isolated as a function of time and multiply bioresources. In addition, the ability of related pig fecal bacteria to degrade and modify the structure of cellulosic biomass were determined. These results will help determine how effective the fermentation of cellulose with SDCC 1b/2a and pig fecal bacterial is on the reactivity and ultrastructure of cellulose.United States. Department of AgricultureUnited States. Agricultural Research Service. Midwest AreaUnited States. Defense Advanced Research Projects Agenc

Abattoir holding pens as a source of Salmonella for swine.

This study was designed to determine if rapid Salmonella infection is possible during the pre-slaughter holding period at swine abattoirs. For 24 groups of pigs studied in 2 high capacity abattoirs, pooled fecal samples were collected from the transport trailer right after pigs were unloaded (pre-holding samples). Holding pens were sampled prior to the entry of study pigs for the pre-slaughter holding. After slaughter, cecal contents and ileocecal lymph nodes were collected from 30 pigs in each studied group (post-holding samples). From all holding pens sampled (100%) at least one Salmonella serovar was isolated. All groups of pigs were Sa/monel/a-positive in the post-holding sampling, including those groups Salmonella-negative in the pre-holding sampling. Some groups had Salmonella serovars that matched serovars isolated from the holding pens, but not with serovars isolated from the pre-holding samples. Results indicate that the abattoir holding pens constitute an important source of Salmonella infections for swine.</p