The Bovine Rumen Microbiome Revealed by Different Fractions of Rumen Contents

The bovine rumen microbiota is very important in terms of animal functionality and digestion. The fermentative capability of the rumen provides means for the digestion of complex plant material that is indigestible by humans. The rumen microbiota is made up of billions of microorganisms, primarily bacteria, that digest and ferment feed into volatile fatty acids and bacterial protein for the animal’s energy and protein needs, respectively. Changes to the rumen microbiota can have a direct measure on animal growth, health, and performance. The possibility of productivity boosts in the cattle industry make the rumen microbiome a hot topic in the field of livestock research. A consistent and accurate method for the fractionation of rumen contents would improve the ability for researchers to detect differences found in rumen microbiomes among different animals and treatments. The objective of this study was to determine the view that five different sampling methods of rumen contents would have on the rumen microbiome. Steers fed hay and fresh pasture wheat were used, which also highlights differences found between diets. Next generation sequencing was used to sequence the V4 region of bacterial 16sRNA. Results were analyzed via Mothur, an open source command-line used to analyze sequencing data in microbial communities, and visualized using R, a command-line software used for statistical analysis and graphical display. The results of this study provided no significant differences between fractionation methods; however, noteworthy differences were observed between the two diets. Due to the lack of differences between methods, the best method was chosen based on time, efficiency, and simplicity. The results of this study allow research scientists to pick the method of choice without sacrificing the accuracy of results

The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons

Bacteria are key in the biodegradation of polycyclic aromatic hydrocarbons (PAH), which are widespread environmental pollutants. At least six genotypes of PAH degraders are distinguishable via phylogenies of the ring-hydroxylating dioxygenase (RHD) that initiates bacterial PAH metabolism. A given RHD genotype can be possessed by a variety of bacterial genera, suggesting horizontal gene transfer (HGT) is an important process for dissemination of PAH-degrading genes. But, mechanisms of HGT for most RHD genotypes are unknown. Here, we report in silico and functional analyses of the phenanthrene-degrading bacterium Delftia sp. Cs1-4, a representative of the phnAFK2 RHD group. The phnAFK2 genotype predominates PAH degrader communities in some soils and sediments, but, until now, their genomic biology has not been explored. In the present study, genes for the entire phenanthrene catabolic pathway were discovered on a novel ca. 232 kb genomic island (GEI), now termed the phn island. This GEI had characteristics of an integrative and conjugative element with a mobilization/stabilization system similar to that of SXT/R391-type GEI. But, it could not be grouped with any known GEI, and was the first member of a new GEI class. The island also carried genes predicted to encode: synthesis of quorum sensing signal molecules, fatty acid/polyhydroxyalkanoate biosynthesis, a type IV secretory system, a PRTRC system, DNA mobilization functions and >50 hypothetical proteins. The 50% G + C content of the phn gene cluster differed significantly from the 66.7% G + C level of the island as a whole and the strain Cs1-4 chromosome, indicating a divergent phylogenetic origin for the phn genes. Collectively, these studies added new insights into the genetic elements affecting the PAH biodegradation capacity of microbial communities specifically, and the potential vehicles of HGT in general

Cystic fibrosis lung microbiome: Opportunities to reconsider management of airway infection

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113756/1/ppul23243.pd

Decomposition in pasture soil receiving excreta from ruminants fed alfalfa forage diet supplemented with increasing proportions of Sericea Lespedeza legume

Healthy soil is fundamental to a productive pasture system as it will decompose labile organic matter and promote retention of carbon to build a stable, resistant pool of organic matter. An easy, standardized approach to measure decomposition and litter stabilization that is gaining popularity in both citizen science and research studies is the use of the Tea Bag Index. The Tea Bag Index is a relatively new method evaluating the loss of organic material in two different kinds of commercial tea bags (green tea and Rooibos tea) after burial in the soil for 90 days. The objective of this experiment was to use the Tea Bag Index to determine if decomposition rate and litter stabilization were affected by inputs of excreta from ruminants fed alfalfa forage diets modified with 0%, 9%, 18%, or 27% of the tannin-containing legume sericea lespedeza, urea, or an untreated negative control in soil plots (n = 4). There was no difference in decomposition rate or litter stabilization among any treatments measured in the 8 cm of surface soil during the first spring growing season after treatment application of excreta or urea to the soil. Results of this experiment indicated that animal amendments simulating urine and manure patches did not result in detectable changes in organic matter decomposition during the first spring season after application to silt loam pasture soil growing tall fescue grass in the mid-South

Development of New Measurements and Tools to Mitigate Fescue Toxicosis in Beef Cattle

The objective of this study was to identify new ways to determine the severity of fescue toxicosis and identify genetic differences in fescue impacted traits as a basis in understanding how cattle could be selected for tolerance to fescue toxicosis. We identified across breed and within breed differences in heat stress related traits and growth rate in pregnant cows exposed to toxic fescue. In addition, new biomarkers were identified to differentiate susceptible and tolerant cattle in the form of specific fecal and vaginal microbes. Finally, we identified differentially expressed (DE) genes in high versus low tolerant cattle on toxic fescue. These findings may allow more accurate diagnosis of fescue toxicosis and provide a glimpse into the genes and microorganisms that may impact tolerance or susceptibility to toxic fescue

Gut Microbiota Is a Major Contributor to Adiposity in Pigs

Different breeds of pigs vary greatly in their propensity for adiposity. Gut microbiota is known to play an important role in modulating host physiology including fat metabolism. However, the relative contribution of gut microbiota to lipogenic characteristics of pigs remains elusive. In this study, we transplanted fecal microbiota of adult Jinhua and Landrace pigs, two breeds of pigs with distinct lipogenic phenotypes, to antibiotic-treated mice. Our results indicated that, 4 weeks after fecal transplantation, the mice receiving Jinhua pigs’ “obese” microbiota (JM) exhibited a different intestinal bacterial community structure from those receiving Landrace pigs’ “lean” microbiota (LM). Notably, an elevated ratio of Firmicutes to Bacteroidetes and a significant diminishment of Akkermansia were observed in JM mice relative to LM mice. Importantly, mouse recipients resembled their respective porcine donors in many of the lipogenic characteristics. Similar to Jinhua pig donors, JM mice had elevated lipid and triglyceride levels and the lipoprotein lipase activity in the liver. Enhanced expression of multiple key lipogenic genes and reduced angiopoietin-like 4 (Angptl4) mRNA expression were also observed in JM mice, relative to those in LM mice. These results collectively suggested that gut microbiota of Jinhua pigs is more capable of enhancing lipogenesis than that of Landrace pigs. Transferability of the lipogenic phenotype across species further indicated that gut microbiota plays a major role in contributing to adiposity in pigs. Manipulation of intestinal microbiota will, therefore, have a profound impact on altering host metabolism and adipogenesis, with an important implication in the treatment of human overweight and obesity

Decade-long bacterial community dynamics in cystic fibrosis airways

The structure and dynamics of bacterial communities in the airways of persons with cystic fibrosis (CF) remain largely unknown. We characterized the bacterial communities in 126 sputum samples representing serial collections spanning 8–9 y from six age-matched male CF patients. Sputum DNA was analyzed by bar-coded pyrosequencing of the V3–V5 hypervariable region of the 16S rRNA gene, defining 662 operational taxonomic units (OTUs) from > 633,000 sequences. Bacterial community diversity decreased significantly over time in patients with typically progressive lung disease but remained relatively stable in patients with a mild lung disease phenotype. Antibiotic use, rather than patient age or lung function,was the primary driver of decreasing diversity. Interpatient variability in community structure exceeded intrapatient variability in serial samples. Antibiotic treatment was associated with pronounced shifts in community structure, but communities showed both short- and longterm resilience after antibiotic perturbation. There was a positive correlation between OTU occurrence and relative abundance, with a small number of persistent OTUs accounting for the greatest abundance. Significant changes in community structure, diversity, or total bacterial density at the time of pulmonary exacerbation were not observed. Despite decreasing community diversity in patients with progressive disease, total bacterial density remained relatively stable over time. These findings show the critical relationship between airway bacterial community structure, disease stage, and clinical state at the time of sample collection. These features are the key parameters with which to assess the complex ecology of the CF airway.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/91945/1/2012 PNAS Decade-long bacterial community dynamics in cystic fibrosis airways.pd

Isolated Rearing at Lactation Increases Gut Microbial Diversity and Post-weaning Performance in Pigs

Environment and diet are two major factors affecting the human gut microbiome. In this study, we used a pig model to determine the impact of these two factors during lactation on the gut microbiome, immune system, and growth performance. We assigned 80 4-day-old pigs from 20 sows to two rearing strategies at lactation: conventional rearing on sow’s milk (SR) or isolated rearing on milk replacer supplemented with solid feed starting on day 10 (IR). At weaning (day 21), SR and IR piglets were co-mingled (10 pens of 4 piglets/pen) and fed the same corn-soybean meal-dried distiller grain with solubles- and antibiotic-free diets for eight feeding phase regimes. Fecal samples were collected on day 21, 62, and 78 for next-generation sequencing of the V4 hypervariable region of the bacterial 16S rRNA gene. Results indicate that IR significantly increased swine microbial diversity and changed the microbiome structure at day 21. Such changes diminished after the two piglet groups were co-mingled and fed the same diet. Post-weaning growth performance also improved in IR piglets. Toward the end of the nursery period (NP), IR piglets had greater average daily gain (0.49 vs. 0.41 kg/d; P < 0.01) and average daily feed intake (0.61 vs. 0.59 kg/d; P < 0.01) but lower feed efficiency (0.64 vs. 0.68; P = 0.05). Consequently, IR piglets were heavier by 2.9 kg (P < 0.01) at the end of NP, and by 4.1 kg (P = 0.08) at market age compared to SR piglets. Interestingly, pigs from the two groups had similar lean tissue percentage. Random forest analysis showed that members of Leuconostoc and Lactococcus best differentiated the IR and SR piglets at weaning (day 21), were negatively correlated with levels of Foxp3 regulatory T cell populations on day 20, and positively correlated with post-weaning growth performance. Our results suggest that rearing strategies may be managed so as to accelerate early-life establishment of the swine gut microbiome to enhance growth performance in piglets

Impact of Enhanced Staphylococcus DNA Extraction on Microbial Community Measures in Cystic Fibrosis Sputum

Staphylococcus aureus is a common constituent of the bacterial community inhabiting the airways of persons with cystic fibrosis (CF). Culture-independent studies have shown that this species is often present in relatively high abundance and would therefore be expected to exert a pronounced effect on measures of CF airway bacterial community structure. We investigated the impact of DNA extraction method on pyrosequencing-based measures of Staphylococcus abundance and bacterial community structure in 17 sputum samples from five CF patients. Staphylococcus was detected in fewer samples when DNA was extracted using a standard bacterial lysis method compared to when DNA was extracted using a lysis buffer amended with lysostaphin and lysozyme. The standard lysis method resulted in significantly lower measures of Staphylococcus relative abundance and higher levels of community diversity, richness, and evenness compared to the lysostaphin-lysozyme modified method. Measures of community dynamics in serial sputum samples from the same individual were nevertheless highly concordant between the two DNA extraction methods. These results illustrate the impact of DNA preparation method on measures of Staphylococcus abundance and bacterial community structures in studies of the airways microbiota in CF