Improved extraction of PCR-quality community DNA from digesta and fecal samples

Populations of select cultured and uncultured bacteria in the rumen of sheep and the effect of diets and ruminal fractions

The objective of this study was to assess the importance of select cultured and uncultured bacteria in the rumen by quantifying their populations and the effect of diets and ruminal fractions. Full-length 16S rRNA gene (rrs) sequences were recovered from rumen samples using specific primers designed from partial sequences recovered previously. Five uncultured bacterial operational taxonomic units (OTUs) were quantified using specific quantitative PCR (qPCR) in fractionated ruminal samples from sheep fed either hay alone or hay plus corn. Species Fibrobacter succinogenes, Ruminococcus albus, R. flavefaciens, Ruminobacter amylophilus, Selenomonas ruminantium, and Mitsuokella multacida and genera Butyrivibrio and Prevotella were also quantified as comparison. The full-length rrs sequence improved taxonomic assignments of partial rrs sequences. Genus Prevotella had the greatest abundance. Of the three major cultured cellulolytic species, R. flavefaciens was most abundant, followed by R. albus and F. succinogenes. The five uncultured bacterial OTUs, classified to genus Acetivibrio, genus Allobaculum, family Ruminococcaceae, order Clostridiales, or class Clostridia, had abundance comparable to that of the above species of genera except Prevotella. Corn supplementation and fractions affected distribution of the rumen bacteria, but to a limited extent. When compared to the qPCR data, sequence frequencies in the rrs clone libraries tended to overestimate the abundance of the bacteria represented. This study showed that abundance and population dynamics of uncultured bacteria can be quantified by specific qPCR, which complements the results of rrs clone libraries. This study also revealed that some uncultured bacteria might be as important as some of the well-characterized bacteria in the rumen. The approach used should be applicable to assess the abundance and potential importance of uncultured bacteria in other environments.

Differences in the rumen methanogen populations of lactating Jersey and Holstein dairy cows under the same diet regimen

In the dairy cattle industry, Holstein and Jersey are the breeds most commonly used for production. They differ in performance by various traits, such as body size, milk production, and milk composition. With increased concerns about the impact of agriculture on climate change, potential differences in other traits, such as methane emission, also need to be characterized further. Since methane is produced in the rumen by methanogenic archaea, we investigated whether the population structure of methanogen communities would differ between Holsteins and Jerseys. Breed-specific rumen methanogen 16S rRNA gene clone libraries were constructed from pooled PCR products obtained from lactating Holstein and Jersey cows, generating 180 and 185 clones, respectively. The combined 365 sequences were assigned to 55 species-level operational taxonomic units (OTUs). Twenty OTUs, representing 85% of the combined library sequences, were common to both breeds, while 23 OTUs (36 sequences) were found only in the Holstein library and 12 OTUs (18 sequences) were found only in the Jersey library, highlighting increased diversity in the Holstein library. Other differences included the observation that sequences with species-like sequence identity to Methanobrevibacter millerae were represented more highly in the Jersey breed, while Methanosphaera-related sequences and novel uncultured methanogen clones were more frequent in the Holstein library. In contrast, OTU sequences with species-level sequence identity to Methanobrevibacter ruminantium were represented similarly in both libraries. Since the sampled animals were from a single herd consisting of two breeds which were fed the same diet and maintained under the same environmental conditions, the differences we observed may be due to differences in host breed genetics.

Mycobacterium behavior in wastewater treatment plant, a bacterial model distinct from Escherichia coli and Enterococci

Mycobacteria are waterborne emerging pathogens causing infections in human. Mycobacteria have been previously isolated from wastewater and sludge, but their densities were not estimated due to cultural biases. In order to evaluate the impact of wastewater treatment processes on mycobacteria removal, we used a real time PCR method. First we compared six DNA extraction methods and second we used the more efficient DNA extraction procedure (i.e., enzymatic lysis combined with hexadecyltrimethylammonium bromide-NaCl procedure) in order to quantify Mycobacterium. With the aim to identify parameters that could serve as indicator of mycobacterial behavior, mycobacterial densities were measured in parallel to those of Escherichia coli and enterococci, and to concentrations of chemical parameters usually monitored in wastewater. Mycobacterium reached 5.5 × 10⁵ ± 3.9 × 10⁵ copies/L in the influent, but was not detected in the effluent after decantation and biofiltration. Most mycobacteria (98.6 ± 2.7%, i.e. 2.4 ± 0.7 log₁₀) were removed by the physical-chemical decantation, and the remaining mycobacteria were removed by biofiltration. In contrast, enterococci and E. coli were lightly removed by decantation step and mainly removed by biofiltration. Our results showed that Mycobacterium corresponds to a hydrophobic behavior linked to insoluble compound removal, whereas enterococci and E. coli refer to hydrophilic behaviors linked to soluble compound removals.

Digestive physiological outcomes related to polydextrose and soluble maize fibre consumption by healthy adult men

The objective of the present study was to evaluate digestive physiological outcomes elicited by functional fibres fed to healthy adult men. A total of twenty-one healthy adult men were utilised in a cross-over design. Each subject received polydextrose (PDX) or soluble maize fibre (SCF) (21 g/d) or no supplemental fibre (no fibre control; NFC) in a snack bar. Periods were 21 d and faeces were collected during the last 5 d of each period. Food intake, including fibre intake, did not differ among treatments. Flatulence (P = 0·001) and distention (P = 0·07) were greatest when subjects consumed PDX or SCF. Reflux was greater (P = 0·04) when subjects consumed SCF compared with NFC. All tolerance scores were low ( < 2·5), indicating only slight discomfort. Faecal ammonia, 4-methylphenol, indole and branched-chain fatty acid concentrations were decreased (P < 0·01) when subjects consumed the functional fibre sources compared with NFC. Faecal acetate, propionate and butyrate concentrations were lower (P < 0·05) when subjects consumed PDX compared with SCF and NFC. Faecal pH was lower (P = 0·01) when subjects consumed SCF compared with NFC, while PDX was intermediate. Faecal wet weight was greatest (P = 0·03) when subjects consumed SCF compared with NFC. Faecal dry weight tended to be greater (P = 0·07) when subjects consumed PDX compared with NFC. The functional fibres led to 1·4 and 0·9 g (PDX and SCF, respectively) increases in faecal dry mass per g supplemental fibre intake. Bifidobacterium spp. concentrations were greater (P < 0·05) when subjects consumed SCF compared with NFC. These functional fibres appear to be beneficial to gut health while leading to minimal gastrointestinal upset.

Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs

The importance of bacteria in the gastrointestinal tracts of animals is widely acknowledged as important. However, very little is known about composition and distribution of the microbial population in lower intestinal tracts of animals. Because most bacterial species in pig intestines have not been cultured, it has been difficult to analyze bacterial diversity by conventional culture methods. Even with the development of culture independent 16S rRNA gene sequencing, the previous methods were slow and labor intensive. Therefore, high throughput pyrosequencing of 16S rDNA libraries was used in this study in order to explore the bacterial diversity of the pig feces. In our two trials, fecal samples from individual pigs were collected five times at 3-week intervals, and the 16S rRNA genes in the community DNAs from fecal samples were sequenced and analyzed. This longitudinal study design identified that microbial populations in the feces of the each pig continued to change as pigs aged. The variations of bacterial diversity of the animals were affected by less abundant bacterial components of the feces. These results help us to understand the age-related bacterial diversity in the commercial pig feces.

Effect of liquid whey feeding on fecal microbiota of mature and growing pigs

The effect of liquid whey feeding on fecal bacteria and their metabolites was assessed in five pregnant sows and 66 growing pigs. Sows were fed a control diet for 4 weeks (control period) followed by the same diet but with whey feeding (5 L/day/pig) for 4 weeks (whey period). One group of growing pigs was given 267 L of whey per pig (whey group), while the other group was not (control group). In both cases, liquid whey was given separately from control diet. Sows in the whey period had feces showing lower pH, lower ammonia concentration, and larger population sizes of total bacteria, lactobacilli and bifidobacteria. The bacterial gene library analysis indicated that Mitsuokella and Megasphaera were more frequently detected, while Clostridium disporicum were detected less frequently in the whey period. Feces from whey-fed growing pigs showed lower pH than that from control pigs in the early stage of growing. Also, larger populations of total bacteria, lactobacilli and bifidobacteria were recorded in the whey group. From the bacterial gene library analysis, the detection frequency of Lactobacillus reuteri tended to be higher in the whey group. These results indicate that whey feeding influences the hindgut microbiota of pigs, possibly leading to a fermentation shift that is favorable for animal health.

Overestimation of the abundance of sulfate-reducing bacteria in human feces by quantitative PCR targeting the Desulfovibrio 16S rRNA gene

The dominant genus of sulfate-reducing bacteria (SRB) in humans is Desulfovibrio, and quantitative PCR (QPCR) targeting the 16S rRNA gene is often used in assays. We show that the 16S rRNA gene assay overestimated SRB abundance in feces from 24 adults compared to QPCR assays using primers targeting two genes involved in SRB energy metabolism.

In vitro digestion and fermentation characteristics of temulose molasses, a coproduct of fiberboard production, and select temulose fractions using canine fecal inoculum

It is of interest to discover new fermentable carbohydrate sources that function as prebiotics. This study evaluated the hydrolytic digestibility, fermentative capacity, and microbiota modulating properties of Temulose molasses, four hydrolyzed fractions of Temulose molasses, short-chain fructooligosaccharides (scFOS), and a yeast cell wall preparation (Safmannan). These substrates resisted in vitro hydrolytic digestion. Each substrate was fermented in vitro using dog fecal inoculum, and fermentation characteristics were quantified at 0 and 12 h. All Temulose molasses substrates decreased pH by at least 0.64 unit and resulted in greater (P < 0.05) butyrate and total short-chain fatty acid (SCFA) production compared to scFOS and Safmannan. Temulose molasses substrates resulted in higher (P < 0.01) or equal Bifidobacterium spp. concentrations compared to scFOS. Temulose molasses substrate and its fractions demonstrated prebiotic characteristics as indicated by low hydrolytic digestibility, high fermentability, and enhanced growth of microbiota considered to be beneficial to health.

Nitrification and denitrification gene abundances in swine wastewater anaerobic lagoons

Although anaerobic lagoons are used globally for livestock waste treatment, their detailed microbial cycling ofN is only beginning to become understood. Within this cycling, nitrification can be performed by organisms that produce the enzyme ammonia monooxygenase. For denitrification, the reduction of nitrite to nitric oxide can be catalyzed by two forms of nitrite reductases, and N,O can be reduced by nitrous oxide reductase encoded by the gene nosZ The objectives of this investigation were to (i) quantify the abundance of the amoA, nirK, nirS, and nosZ genes; (ii) evaluate the influence of environmental conditions on their abundances; and (iii) evaluate their abundance relative to denitrification enzyme activity (DEA). Samples were analyzed via real-time quantitative polymerase chain reaction and collected from eight typical, commercial anaerobic, swine wastewater lagoons located in the Carolinas. The four genes assayed in this study were present in all eight lagoons. Their abundances relative to total bacterial populations were 0.04% (amoA), 1.33% (nirS), 5.29% (nirK), and 0.27% (nosZ). When compared with lagoon chemical characteristics, amoA and nirK correlated with several measured variables. Neither nirS nor nosZ correlated with any measured environmental variables. Although no gene measured in this study correlated with actual or potential DEA, nosZ copy numbers did correlate with the disparity between actual and potential DEA. Phylogenetic analysis ofnosZdid not reveal any correlations to DEA rates. As with other investigations, analyses of these genes provide useful insight while revealing the underlying greater complexity of N cycling within swine waste lagoons.

Effects of methanogenic inhibitors on methane production and abundances of methanogens and cellulolytic bacteria in in vitro ruminal cultures

The objective of this study was to systematically evaluate and compare the effects of select antimethanogen compounds on methane production, feed digestion and fermentation, and populations of ruminal bacteria and methanogens using in vitro cultures. Seven compounds, including 2-bromoethanesulphonate (BES), propynoic acid (PA), nitroethane (NE), ethyl trans-2-butenoate (ETB), 2-nitroethanol (2NEOH), sodium nitrate (SN), and ethyl-2-butynote (EB), were tested at a final concentration of 12 mM. Ground alfalfa hay was included as the only substrate to simulate daily forage intake. Compared to no-inhibitor controls, PA, 2NEOH, and SN greatly reduced the production of methane (70 to 99%), volatile fatty acids (VFAs; 46 to 66%), acetate (30 to 60%), and propionate (79 to 82%), with 2NEOH reducing the most. EB reduced methane production by 23% without a significant effect on total VFAs, acetate, or propionate. BES significantly reduced the propionate concentration but not the production of methane, total VFAs, or acetate. ETB or NE had no significant effect on any of the above-mentioned measurements. Specific quantitative-PCR (qPCR) assays showed that none of the inhibitors significantly affected total bacterial populations but that they did reduce the Fibrobacter succinogenes population. SN reduced the Ruminococcus albus population, while PA and 2NEOH increased the populations of both R. albus and Ruminococcus flavefaciens. Archaeon-specific PCR-denaturing gradient gel electrophoresis (DGGE) showed that all the inhibitors affected the methanogen population structure, while archaeon-specific qPCR revealed a significant decrease in methanogen population in all treatments. These results showed that EB, ETB, NE, and BES can effectively reduce the total population of methanogens but that they reduce methane production to a lesser extent. The results may guide future in vivo studies to develop effective mitigation of methane emission from ruminants.

High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut

Recent studies have shown the microbial biofilms adherent to plant biomass in the gastrointestinal tracts of humans and other herbivores are quite different to planktonic populations. If these biofilm communities are to be properly characterized by metagenomics methods, then the microbial desorption methods used must ensure the phylogenetic diversity and genetic potential recovered is biologically valid. To that end, we describe here two different methods for desorbing microbes tightly adherent to plant biomass; and used PCR-DGGE analyses of the Bacteria and Archaea rrs genes to show both these desorption methods were effective in recovering the adherent microbial biofilm with no apparent biases in microbe recovery. We also present a derivation of the "repeated bead beating and column (RBB+C) purification" method of DNA extraction that results in the recovery of high molecular weight DNA. These DNA samples can be fragmented and size fractionated by sucrose density gradient centrifugation, bypassing the use of gel-plug lysis and pulsed-field gel electrophoresis separation of DNA for metagenomic library constructions.

The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue

Potentially valuable sources of DNA have been extracted from human colonic tissues and are retained in biobanks throughout the world, and might be re-examined to better understand host-microbe interactions in health and disease. However, the published protocols for DNA extraction typically used by gastroenterologists have not been systematically compared in terms of their recovery of the microbial fraction associated with colonic tissue. For this reason, we examined how three different tissue DNA extraction methods (the QIAGEN AllPrep DNA/RNA kit, salting out and high molecular weight (HMW) methods of DNA extraction) employed in past clinical trials, and the repeated bead beating and column (RBB+C) method might impact the recovery of microbial DNA from colonic tissue, using a custom designed phylogenetic microarray for gut bacteria and archaea. All four methods produced very similar profiles of the microbial diversity, but there were some differences in probe signal intensities, with the HMW method producing stronger probe intensities for a subset of the Firmicutes probes including Clostridium and Streptococcus spp. Real-time PCR analysis revealed that the HMW and RBB+C extracted DNA contained significantly more DNA of Firmicutes origin and that the different DNA extraction methods also gave variable results in terms of host DNA recovery. All of the methods tested recovered DNA from the archaeal community although there were some differences in probe signal intensity. Based on these findings, we conclude that while all four methods are efficacious at releasing microbial DNA from biopsy tissue samples, the HMW and RBB+C methods of DNA extraction may release more DNA from some of the Firmicutes bacteria associated with colonic tissue. Thus, DNA archived in biobanks could be suitable for retrospective profiling analyses, provided the caveats with respect to the DNA extraction method(s) used are taken into account.

Quantification of butyryl CoA:acetate CoA-transferase genes reveals different butyrate production capacity in individuals according to diet and age

The gastrointestinal microbiota produces short-chain fatty acids, especially butyrate, which affect colonic health, immune function and epigenetic regulation. To assess the effects of nutrition and aging on the production of butyrate, the butyryl-CoA:acetate CoA-transferase gene and population shifts of Clostridium clusters lV and XlVa, the main butyrate producers, were analysed. Faecal samples of young healthy omnivores (24 ± 2.5 years), vegetarians (26 ± 5 years) and elderly (86 ± 8 years) omnivores were evaluated. Diet and lifestyle were assessed in questionnaire-based interviews. The elderly had significantly fewer copies of the butyryl-CoA:acetate CoA-transferase gene than young omnivores (P=0.014), while vegetarians showed the highest number of copies (P=0.048). The thermal denaturation of the butyryl-CoA:acetate CoA-transferase gene variant melting curve related to Roseburia/Eubacterium rectale spp. was significantly more variable in the vegetarians than in the elderly. The Clostridium cluster XIVa was more abundant in vegetarians (P=0.049) and in omnivores (P<0.01) than in the elderly group. Gastrointestinal microbiota of the elderly is characterized by decreased butyrate production capacity, reflecting increased risk of degenerative diseases. These results suggest that the butyryl-CoA:acetate CoA-transferase gene is a valuable marker for gastrointestinal microbiota function.

Phylogenetic diversity and dietary association of rumen Treponema revealed using group-specific 16S rRNA gene-based analysis

Treponema spp. are a commonly detected bacterial group in the rumen that are involved in the degradation of soluble fibers. In this study, a ruminal Treponema group-specific PCR primer targeting the 16S rRNA gene was designed and used to assess the phylogenetic diversity and diet association of this group in sheep rumen. Total DNA was extracted from rumen digesta of three sheep fed a diet based on alfalfa/orchardgrass hay or concentrate. The real-time PCR quantification indicated that the relative abundance of the Treponema group in the total rumen bacteria was as high as 1.05%, while the known species Treponema bryantii accounted for only 0.02%. Fingerprints of the Treponema community determined by 16S rDNA-targeted denaturing gradient gel electrophoresis (DGGE) analysis tended to differ among the diets. Principal component analysis of the DGGE profiles distinguished those Treponema associated with either the hay or the concentrate diets. Analysis of a Treponema 16S rRNA gene clone library showed phylogenetically distinct operational taxonomic units for a specific dietary condition, and significant (P=0.001) differences in community composition were observed among clone libraries constructed from each dietary regimen. The majority of clones (75.4%) had <97% sequence similarity with known Treponema. These results suggest the predominance of uncultured Treponema that appear to have distinct members related to the digestion of either hay or concentrate diet.

Effects of short-chain fructooligosaccharides and galactooligosaccharides, individually and in combination, on nutrient digestibility, fecal fermentative metabolite concentrations, and large bowel microbial ecology of healthy adults cats

Short-chain fructooligosaccharides (scFOS) and galactooligosaccharides (GOS) are nondigestible oligosaccharides that result in a prebiotic effect in some animal species; however, the cat has not been well studied in this regard. This experiment evaluated scFOS and GOS supplementation on nutrient digestibility, fermentative end product production, and fecal microbial ecology of cats. Eight healthy adult cats were fed diets containing no prebiotic, 0.5% scFOS, 0.5% GOS, or 0.5% scFOS + 0.5% GOS (scFOS + GOS) in a replicated 4 × 4 Latin square design. Apparent total tract CP digestibility was decreased (P < 0.05) when cats were fed a diet containing scFOS + GOS compared with the other treatments. Dry matter, OM, acid hydrolyzed fat, and GE digestibilities were not different (P > 0.05) among treatments. Cats fed scFOS-, GOS-, and scFOS + GOS-supplemented diets had greater (P < 0.05) fecal Bifidobacterium spp. populations compared with cats fed the control diet. Fecal pH was less (P < 0.05) for cats fed the scFOS + GOS-supplemented diet compared with the control. Butyrate (P = 0.05) and valerate (P < 0.05) concentrations were greater when cats consumed the scFOS + GOS diet. Acetate tended (P = 0.10) to be greater when cats were fed the scFOS + GOS diet. Total short-chain fatty acid (P = 0.06) and total branched-chain fatty acid (P = 0.06) concentrations also tended to be greater when cats consumed the scFOS + GOS treatment. Fecal protein catabolites, including ammonia, 4-methylphenol, indole, and biogenic amines, blood lymphocytes, neutrophils, total white blood cell counts, or fecal DM concentration and output did not differ (P > 0.05) among treatments. Low level supplementation of scFOS, GOS, and their combination exert positive effects on select indices of gut health in cats.

Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. II. Protozoa population and diversity of bacterial communities

Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of dietary characteristics on microbial populations and bacterial diversity. The purpose of the study was to assess how closely fermenters can mimic the differences between diets found in vivo. The 4 experimental diets contained forage to concentrate (F:C) ratios of 70:30 (high forage; HF) or 30:70 (high concentrate; HC) with either alfalfa hay (A) or grass hay (G) as the forage. Total bacterial numbers were greater in the rumen of sheep fed HF diets compared with those fed HC diets, whereas the opposite was found in fermenters. The numbers of cellulolytic bacteria were not affected by F:C ratio in any fermentation system, but cellulolytic numbers were 2.7 and 1.8 times greater in sheep than in fermenters for HF and HC diets, respectively. Neither total bacterial nor cellulolytic numbers were affected by the type of forage in sheep or fermenters. Decreasing F:C ratio increased total protozoa and Entodiniae numbers in sheep by about 29 and 25%, respectively, but it had no effect in fermenters. Isotrichidae and Ophryoscolecinae numbers in sheep were not affected by changing F:C ratio, but both disappeared completely from fermenters fed HC diets. Total protozoa and Entodiniae numbers were greater in sheep fed A diets than in those fed G diets, whereas the opposite was found in fermenters. Results indicate that under the conditions of the present study, protozoa population in Rusitec fermenters was not representative of that in the rumen of sheep fed the same diets. In addition, protozoa numbers in fermenters were 121 and 226 times lower than those in the sheep rumen for HF and HC diets, respectively. The automated ribosomal intergenic spacer analysis of the 16S ribosomal DNA was used to analyze the diversity of liquid- and solid-associated bacteria in both systems. A total of 170 peaks were detected in the automated ribosomal intergenic spacer analysis electropherograms of bacterial pellets across the full set of 64 samples, from which 160 were detected in at least 1 individual from each system (sheep or fermenter). Diversity of liquid-associated bacterial pellets was greater with G diets in fermenters but seemed to be unaffected by diet in sheep. Bacterial diversity in solid-associated bacteria pellets was greater for G diets compared with A diets in sheep and fermenters. Different conditions in the fermenters compared with sheep rumen might have caused a selection of some bacterial strains.

Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice

This study is the first to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gastrointestinal microbiome. Six healthy adult dogs were used in a crossover design and fed a low-fiber control diet (K9C) or one containing 7.5% beet pulp (K9BP). Pooled fecal DNA samples from each treatment were subjected to 454 pyrosequencing, generating 503 280 (K9C) and 505 061 (K9BP) sequences. Dominant bacterial phyla included the Bacteroidetes/Chlorobi group and Firmicutes, both of which comprised ∼35% of all sequences, followed by Proteobacteria (13–15%) and Fusobacteria (7–8%). K9C had a greater percentage of Bacteroidetes, Fusobacteria and Proteobacteria, whereas K9BP had greater proportions of the Bacteroidetes/Chlorobi group and Firmicutes. Archaea were not altered by diet and represented ∼1% of all sequences. All archaea were members of Crenarchaeota and Euryarchaeota, with methanogens being the most abundant and diverse. Three fungi phylotypes were present in K9C, but none in K9BP. Less than 0.4% of sequences were of viral origin, with >99% of them associated with bacteriophages. Primary functional categories were not significantly affected by diet and were associated with carbohydrates; protein metabolism; DNA metabolism; cofactors, vitamins, prosthetic groups and pigments; amino acids and derivatives; cell wall and capsule; and virulence. Hierarchical clustering of several gastrointestinal metagenomes demonstrated phylogenetic and metabolic similarity between dogs, humans and mice. More research is required to provide deeper coverage of the canine microbiome, evaluate effects of age, genetics or environment on its composition and activity, and identify its role in gastrointestinal disease.

Occurrence and persistence of erythromycin resistance genes (erm) and tetracycline resistance genes (tet) in waste treatment systems on swine farms

Animal manure from modern animal agriculture constitutes the single largest source of antibiotic resistance (AR) owing to the use of large quantities of antibiotics. After animal manure enters the environment, the AR disseminates into the environment and can pose a potentially serious threat to the health and well-being of both humans and animals. In this study, we evaluated the efficiency of three different on-farm waste treatment systems in reducing AR. Three classes of erythromycin resistance genes (erm) genes (B, F, and X) conferring resistances to macrolide-lincosamides-streptogramin B (MLS(B)) and one class of tetracycline resistance genes (tet) gene (G) conferring resistance to tetracyclines were used as models. Real-time polymerase chain reaction assays were used to determine the reservoir sizes of these AR genes present in the entire microbiome. These classes of AR genes varied considerably in abundance, with erm(B) being more predominant than erm(F), erm(X), and tet(G). These AR genes also varied in persistence in different waste treatment systems. Aerobic biofiltration reduced erm(X) more effectively than other AR genes, while mesophilic anaerobic digestion and lagoon storage did not appreciably reduce any of these AR genes. Unlike chemical pollutants, some AR genes could increase after reduction in a preceding stage of the treatment processes. Season might also affect the persistence of AR. These results indicate that AR arising from swine-feeding operations can survive typical swine waste treatment processes and thus treatments that are more effective in destructing AR on farms are required.

Tetracycline resistance associated with commensal bacteria from representative ready-to-consume deli and restaurant foods

Proper knowledge of antibiotic resistance (AR) dissemination is essential for effective mitigation. This study examined the profiles of tetracycline-resistant (Tetr) commensal bacteria from representative ready-to-consume food samples from salad bars at local grocery stores and restaurants. Out of 900 Tetr isolates examined, 158 (17.6%) carried one or more of tetM, tetL, tetS, and tetK genes by conventional PCR, 28 harbored more than one Tetr determinants. The most prevalent genotype was tetM, which was detected in 70.9% of the AR gene carriers, followed by tetL (31.6%), tetS (13.9%), and tetK (2.5%). Identified AR gene carriers included Enterococcus, Lactococcus, Staphylococcus, Brochothrix, Carnobacterium, Stenotrophomonas, Pseudomonas, and Sphingobacterium, by 16S rRNA gene sequence analysis. AR determinants were successfully transmitted, and led to resistance in Streptococcus mutans via natural gene transformation and Enterococcus faecalis via electroporation, suggesting the functionality and mobility of the AR genes from the food commensal bacteria. In addition, the AR traits in many isolates are quite stable, even in the absence of the selective pressure. The identification of new commensal carriers for representative AR genes revealed the involvement of a broad spectrum of bacteria in the horizontal transmission of AR genes. Meanwhile, the spectrum of the antibiotic-resistant bacteria differed from the spectrum of the total bacteria (by denaturing gradient gel electrophoresis) associated with the food items. Our data revealed a common avenue in AR exposure and will assist in proper risk assessment and the development of comprehensive mitigation strategies to effectively combat AR.

Galactoglucomannan oligosaccharide supplementation affects nutrient digestibility, fermentation end-product production, and large bowel microbiota of the dog

A galactoglucomannan oligosaccharide (GGMO) obtained from fiberboard production was evaluated as a dietary supplement for dogs. The GGMO substrate contained increased concentrations of oligosaccharides containing mannose, xylose, and glucose, with the mannose component accounting for 35% of DM. Adult dogs assigned to a 6 × 6 Latin square design were fed 6 diets, each containing a different concentration of supplemental GGMO (0, 0.5, 1, 2, 4, and 8%) that replaced dietary cellulose. Total tract DM and OM apparent digestibilities increased (P < 0.001) linearly, whereas total tract CP apparent digestibility decreased (P < 0.001) linearly as dietary GGMO substrate concentration increased. Fecal concentrations of acetate, propionate, and total short-chain fatty acids increased (P ≤ 0.001) linearly, whereas butyrate concentration decreased (P ≤ 0.001) linearly with increasing dietary concentrations of GGMO. Fecal pH decreased (P ≤ 0.001) linearly as dietary GGMO substrate concentration increased, whereas fecal score increased quadratically (P ≤ 0.001). Fecal phenol (P ≤ 0.05) and indole (P ≤ 0.01) concentrations decreased linearly with GGMO supplementation. Fecal biogenic amine concentrations were not different among treatments except for phenylethylamine, which decreased (P < 0.001) linearly as dietary GGMO substrate concentration increased. Fecal microbial concentrations of Escherichia coli, Lactobacillus spp., and Clostridium perfringens were not different among treatments. A quadratic increase (P ≤ 0.01) was noted for Bifidobacterium spp. as dietary GGMO substrate concentration increased. The data suggest positive nutritional properties of supplemental GGMO when incorporated in a good-quality dog food.

Interrelations between the microbiotas in the litter and in the intestines of commercial broiler chickens

The intestinal microbiota of broiler chickens and the microbiota in the litter have been well studied, but the interactions between these two microbiotas remain to be determined. Therefore, we examined their reciprocal effects by analyzing the intestinal microbiotas of broilers reared on fresh pine shavings versus reused litter, as well as the litter microbiota over a 6-week cycle. Composite ileal mucosal and cecal luminal samples from birds (n = 10) reared with both litter conditions (fresh versus reused) were collected at 7, 14, 21, and 42 days of age. Litter samples were also collected at days 7, 14, 21, and 42. The microbiotas were profiled and compared within sample types based on litter condition using PCR and denaturing gradient gel electrophoresis (PCR-DGGE). The microbiotas were further analyzed using 16S rRNA gene clone libraries constructed from microbiota DNA extracted from both chick intestinal and litter samples collected at day 7. Results showed significant reciprocal effects between the microbiotas present in the litter and those in the intestines of broilers. Fresh litter had more environmental bacteria, while reused litter contained more bacteria of intestinal origin. Lactobacillus spp. dominated the ileal mucosal microbiota of fresh-litter chicks, while a group of bacteria yet to be classified within Clostridiales dominated in the ileal mucosal microbiota in the reused-litter chicks. The Litter condition (fresh versus reused) seemed to have a more profound impact on the ileal microbiota than on the cecal microbiota. The data suggest that the influence of fresh litter on ileal microbiota decreased as broilers grew, compared with temporal changes observed under reused-litter rearing conditions.

Dietary cellulose, fructooligosaccharides, and pectin modify fecal protein catabolites and microbial populations in adult cats

Twelve young adult (1.7 +/- 0.1 yr) male cats were used in a replicated 3 x 3 Latin square design to determine the effects of fiber type on nutrient digestibility, fermentative end products, and fecal microbial populations. Three diets containing 4% cellulose, fructooligosaccharides (FOS), or pectin were evaluated. Feces were scored based on the 5-point system: 1 being hard, dry pellets, and 5 being watery liquid that can be poured. No differences were observed (P > 0.100) in intake of DM, OM, CP, or acid-hydrolyzed fat; DM or OM digestibility; or fecal pH, DM%, output on an as-is or DM basis, or concentrations of histamine or phenylalanine. Crude protein and fat digestibility decreased (P = 0.079 and 0.001, respectively) in response to supplementation with pectin compared with cellulose. Both FOS and pectin supplementation resulted in increased fecal scores (P < 0.001) and concentrations of ammonia (P = 0.003) and 4-methyl phenol (P = 0.003). Fecal indole concentrations increased (P = 0.049) when cats were supplemented with FOS. Fecal acetate (P = 0.030), propionate (P = 0.035), and total short-chain fatty acid (P = 0.016) concentrations increased in pectin-supplemented cats. Fecal butyrate (P = 0.010), isobutyrate (P = 0.011), isovalerate (P = 0.012), valerate (P = 0.026), and total branched-chain fatty acids + valerate (P = 0.008) concentrations increased with supplementation of FOS and pectin. Fecal cadaverine (P < 0.001) and tryptamine (P < 0.001) concentrations increased with supplementation of FOS and pectin. Fecal tyramine concentrations decreased (P = 0.039) in FOS-supplemented cats, whereas spermidine concentrations increased (P < 0.001) in pectin-supplemented cats. Whereas fecal concentrations of putrescine (P < 0.001) and total biogenic amines (P < 0.001) increased with FOS and pectin, the concentrations of these compounds were increased (P < 0.001) in cats supplemented with pectin. Fecal Bifidobacterium spp. concentrations increased (P = 0.006) and Escherichia coli concentrations decreased (P < 0.001) in FOS-supplemented cats. Fecal concentrations of Clostridium perfringens (P < 0.001), E. coli (P < 0.001), and Lactobacillus spp. (P = 0.030) also increased in pectin-supplemented cats. In addition to increasing populations of protein-fermenting microbiota, pectin increased production of fermentative end products associated with carbohydrate compared with protein fermentation. Pectin and FOS may be useful fiber sources in promoting intestinal health of the cat.

Bacterial diversity dynamics in rumen epithelium of wethers fed forage and mixed concentrate forage diets

Cereal-rich diets used in ruminant intensive production can affect the physiology of the rumen wall but little is known about the changes induced to the epimural bacterial community. Dynamics in epimural bacteria was monitored by PCR-DGGE on four wethers fed forage for 20 weeks (constant diet) and on four wethers fed successively forage, a high concentrate diet (65% wheat) and forage for 4, 8 and 8 weeks, respectively (variable diet group). In the constant diet group, no changes were observed throughout time. In contrast, in the variable diet group, the community tended to differ between high concentrate and forage samples (P=0.06). For both groups, the structure of the community was strongly associated to individual hosts (P=0.001). This difference between individuals could have masked the effect of cereal on the variable diet group. To get more information on the phylotypes present, 120 16S rDNA gene clones were sequenced from the rumen epithelium of a wether fed forage and cereal-rich diets. Firmicutes, Bacteroidetes, and Proteobacteria were the predominant phyla but the bacterial types detected were in general different from those commonly found in rumen contents with a high proportion of Proteobacteria (14%) in the rumen epithelium. In the forage periods, Firmicutes represented nearly 50% of the total epimural community and Bacteroidetes were about 33%, while in the concentrate-rich diet period these percentages were inversed (P<0.05). Clone libraries seemed more sensitive than PCR-DGGE to study the bacteria attached to the rumen epithelium. The role of epimural bacteria on ruminant's health needs further investigation.

Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing

Background

Dogs suffer from many of the same maladies as humans that may be affected by the gut microbiome, but knowledge of the canine microbiome is incomplete. This work aimed to use 16S rDNA tag pyrosequencing to phylogenetically characterize hindgut microbiome in dogs and determine how consumption of dietary fiber affects community structure.

Principal Findings

Six healthy adult dogs were used in a crossover design. A control diet without supplemental fiber and a beet pulp-supplemented (7.5%) diet were fed. Fecal DNA was extracted and the V3 hypervariable region of the microbial 16S rDNA gene amplified using primers suitable for 454-pyrosequencing. Microbial diversity was assessed on random 2000-sequence subsamples of individual and pooled DNA samples by diet. Our dataset comprised 77,771 reads with an average length of 141 nt. Individual samples contained approximately 129 OTU, with Fusobacteria (23 – 40% of reads), Firmicutes (14 – 28% of reads) and Bacteroidetes (31 – 34% of reads) being co-dominant phyla. Feeding dietary fiber generally decreased Fusobacteria and increased Firmicutes, but these changes were not equally apparent in all dogs. UniFrac analysis revealed that structure of the gut microbiome was affected by diet and Firmicutes appeared to play a strong role in by-diet clustering.

Conclusions

Our data suggest three co-dominant bacterial phyla in the canine hindgut. Furthermore, a relatively small amount of dietary fiber changed the structure of the gut microbiome detectably. Our data are among the first to characterize the healthy canine gut microbiome using pyrosequencing and provide a basis for studies focused on devising dietary interventions for microbiome-associated diseases.

Carbohydrates blended with polydextrose lower gas production and short-chain fatty acid production in an in vitro system

Maximizing health benefits of prebiotics, while limiting negative side effects, is of importance to the food industry. This study examined several oligosaccharides and their blends in an in vitro fermentation model. Substrates included medium- and long-chain fructooligosaccharides (FOS), oligofructose-enriched inulin, galactooligosaccharide, polydextrose (POL), and 50:50 substrate blends. Substrates and blends were fermented in vitro using human fecal inoculum, and fermentation characteristics were quantified at 0, 4, 8, and 12 hours. We hypothesized that mixtures of short- and long-chain oligosaccharides would generate less gas than do short-chain oligosaccharides and modulate gut microflora to a greater extent than do long-chain oligosaccharides. Carbohydrates blended with POL had decreased (P < .01) total gas volume and H(2) produced after 4, 8, and 12 hours of fermentation compared with individual carbohydrates. Mixing of 2 oligofructose-enriched inulin products led to less (P < .05) gas produced and a slower (P < .05) rate of production. When mixed with POL, all carbohydrates tested in the present study produced less total short-chain fatty acids (P < .04) and butyrate (P < .0001) after 12 hours of in vitro fermentation, compared with individual carbohydrates. The bifidogenic effect of medium-chain FOS and oligofructose-enriched inulin after 12 hours of in vitro fermentation was lower (P < .05) when mixed with POL. Mixing the pure carbohydrates with galactooligosaccharide increased (P < .05) bifidobacteria counts measured after 12 hours of in vitro fermentation, except when mixed with medium-chain FOS. In general, when mixed with POL, all carbohydrates had lower gas production, gas production rates, butyrate and total short-chain fatty acid production, and bifidobacteria counts than when fermented alone for 12 hours.

Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis

Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects (Pearson correlations >0.899 and 0.735, respectively). A detailed comparative analysis of mechanical and enzymatic methods showed that despite their overall similarity, the mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria, including Clostridium cluster IV. By applying the mechanical disruption method a high prevalence (67%) of methanogenic archaea was detected in healthy subjects (n=24), exceeding the typical values reported previously. The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories.

Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis

16S rRNA gene-based analysis of rumen Prevotella was carried out to estimate the diversity and diet specificity of bacteria belonging to this genus. Total DNA was extracted from the rumen digesta of three sheep fed two diets with different hay-to-concentrate ratios (10 : 1 and 1 : 2). Real-time PCR quantification of Prevotella revealed that the relative abundance of this genus in the total rumen bacteria was up to 19.7%, while the representative species Prevotella bryantii and Prevotella ruminicola accounted for only 0.6% and 3.8%, respectively. Denaturing gradient gel electrophoresis analysis for Prevotella revealed shifts in the community composition with the diet. Analysis of 16S rRNA gene clone libraries showed significant differences (P=0.001) between clones detected from the sheep on the diets with different hay-to-concentrate ratios. The majority (87.8%) of Prevotella clones had <97% sequence similarity with known rumen Prevotella. These data suggest that uncultured Prevotella is more abundant than known Prevotella and that members of this genus appear to have specific metabolic niches.

Preliminary study of the changes in rumen bacterial populations from cattle intoxicated with young oak (Quercus pyrenaica) leaves

Intoxication of grazing cattle occurs repeatedly when they consume large amounts of young oak leaves (OL), which are rich in hydrolysable tannins (HT), due to a shortage of other feed resources. The HT are antimicrobial, although some rumen bacteria can resist or degrade them into potentially toxic or harmless metabolites. To study the effect of the administration of HT-rich OL (Quercus pyrenaica) after a severe feed restriction on the rumen bacterial community and monitor the variations in some bacterial groups that are potentially able to resist or metabolise tannins, three ruminally cannulated bulls were initially fed grass hay and then subjected to a severe 8-day feed restriction period, before receiving OL for 6 days. Then, the animals were again offered grass hay for 12 more days. Rumen contents were sampled throughout the experiment. Quantitative real-time polymerase chain reaction and terminal restriction fragment length polymorphism were used to monitor the bacterial dynamics. Animal 1 was not intoxicated and showed lower relative abundances of Streptococcus bovis initially and after the OL administration than Animals 2 and 3, which showed acute signs of intoxication. The genus Prevotella increased its abundance with the OL administration, whereas Selenomonas ruminantium was reduced. The bacterial terminal restriction fragment length polymorphism profile of Animal 1 clustered initially separately from Animals 2 and 3 and was less affected by the feed restriction period. These results showed that the effect of the consumption of HT-rich OL after a severe feed restriction is highly variable in cattle and might rely on the individual composition of the microbiota colonising the rumen.

DNA extraction from bovine faeces: current status and future trends

There is an increasing interest in the detection and enumeration of micro-organisms pathogenic for human and present in bovine faeces. This interest is because pollution of the environment by animal faeces may affect the safety of food and of drinking or recreational water. Detection and quantification of microbial pathogens carried out using DNA extracted from the faecal matrix are affected by the quality and the quantity of the DNA extracts, which are critical factors that limit the accuracy and sensitivity of molecular studies. This review compares published methods on DNA extraction from bovine faeces, focusing on the extent to which the success of DNA amplification is affected by issues related to the faeces. Following a general discussion on the DNA extraction methods used for faeces, we focus particularly on issues related to the faecal environment itself. The objective is to identify information that can be used to improve the sensitivity of those PCR methods used after direct DNA extraction.

High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol

Background

The low and variable prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae DNA in human stool contrasts with the paramount role of these methanogenic Archaea in digestion processes. We hypothesized that this contrast is a consequence of the inefficiencies of current protocols for archaeon DNA extraction. We developed a new protocol for the extraction and PCR-based detection of M. smithii and M. stadtmanae DNA in human stool.

Methodology/Principal Findings

Stool specimens collected from 700 individuals were filtered, mechanically lysed twice, and incubated overnight with proteinase K prior to DNA extraction using a commercial DNA extraction kit. Total DNA was used as a template for quantitative real-time PCR targeting M. smithii and M. stadtmanae 16S rRNA and rpoB genes. Amplification of 16S rRNA and rpoB yielded positive detection of M. smithii in 95.7% and M. stadtmanae in 29.4% of specimens. Sequencing of 16S rRNA gene PCR products from 30 randomly selected specimens (15 for M. smithii and 15 for M. stadtmanae) yielded a sequence similarity of 99–100% using the reference M. smithii ATCC 35061 and M. stadtmanae DSM 3091 sequences.

Conclusions/Significance

In contrast to previous reports, these data indicate a high prevalence of the methanogens M. smithii and M. stadtmanae in the human gut, with the former being an almost ubiquitous inhabitant of the intestinal microbiome.

Selected antimicrobial resistance during composting of manure from cattle administered sub-therapeutic antimicrobials

Composting is being increasingly employed for the recycling of nutrients in manure from the livestock industry. However, composting manure from animals fed antimicrobials has not been well characterized. In this study, compost windrows were prepared using manure collected from cattle (Bos Taurus L.) fed tylosin (TY), chlortetracycline-sulphamethazine (TS), and control cattle (no antimicrobials). The objectives of the 18-wk trial were to quantitatively assess the survival of total E. coli, E. coli resistant to ampicillin (Amp(r)) and tetracycline (Tet(r)), and select tetracycline (tet) and erythromycin resistance methylase (erm) genes. We found that while compost windrows did not reach the recommended temperature of 55 degrees C for 15 d, composting reduced high initial levels of total, Amp(r), and Tet(r) E. coli as early as Week 2. A significant antimicrobial effect on total (P = 0.04) and Amp(r) (P = 0.03) E. coli was observed. Significant antimicrobial x time interactions were observed from Week 0 to Week 3 (Total E. coli: P = 0.04; Amp(r): P = 0.02; Tet(r): P = <0.001). Low absolute abundance of tet and erm genes (<10(6) copies g(-1)) was found and the resistance genes displayed different dynamics; tet(A,C) and erm(A) increased marginally at Week 11 relative to Week 0 and 5 and the remaining genes (tet(G), RPP tet, erm(B), erm(C), erm(F), erm(T), and erm(X)) decreased for most time points and treatments. These results indicate that even though composting reduces antimicrobial resistant E. coli, tet and erm genes could still be detected. Our experiments reiterate advantages of polymerase chain reaction (PCR)-based quantitative assays over cultivation-based methods for the rapid identification of composting effectiveness in eliminating resistance genes before land application.

Evaluation of procedures for detaching particle-associated microbes from forage and concentrate incubated in Rusitec fermenters: efficiency of recovery and representativeness of microbial isolates

Three detachment procedures (DP) were evaluated for their ability to remove particle-associated microbes from digesta in Rusitec fermenters fed a 30:70 alfalfa hay:concentrate diet. Forage and concentrate were incubated in separate nylon bags, and incubation residues were treated independently. Microbial biomass was labeled with (15)NH(4)Cl. Treatments were 1) MET: residues were incubated at 38 degrees C for 15 min with saline solution (0.9% NaCl) containing 0.1% methylcellulose with continuous shaking; 2) STO: residues were mixed with cold saline solution and homogenized with a stomacher for 5 min at 230 revolutions per min; and 3) FRE: residues were immediately frozen at -20 degrees C for 72 h, thawed at 4 degrees C, mixed with saline solution, and subjected to STO procedure. Common to all treatments was storing at 4 degrees C for 24 h after the treatment, homogenization, filtration, and resuspension of residues 2 times in the treatment solutions. Microbial pellets were obtained by centrifugation, and microbial removal was estimated indirectly by measuring removal of (15)N. The PCR-single-stranded conformation polymorphism analysis of the 16S ribosomal DNA was used to analyze the similarity between microbial communities attached to the substrate and those in the pellet obtained after each DP. There were no feed x DP interactions (P = 0.16 to 0.96) for any variable, except for N content in microbial pellets (P = 0.02). Detaching efficiency (P = 0.004) and total recovery (P = 0.01) were affected by DP, with STO showing the greatest values (mean values across substrates of 64.1% for detaching efficiency and 58.3% for total recovery) and MET the least values (57.0 and 51.8%). Similarity index between the microbes attached to substrates and those in the pellets were affected (P = 0.02) by DP, with MET showing greater (P < 0.02) values (84.0 and 86.4% for forage and concentrate, respectively) than FRE (72.5 and 67.8%) and STO having intermediate values (77.1 and 82.4%). There were no differences (P = 0.70) among particle-associated microbe pellets in their N content, but MET pellets had greater (P < 0.05) (15)N enrichments than those obtained by STO and FRE. Although STO was the most effective method to detach ruminal microbes from concentrate and forage, MET produced pellets with the greatest similarity to the microbial communities attached to the substrates and therefore could be considered the most appropriate DP method for treating digesta from Rusitec fermenters.

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).

Diversity of beta-propeller phytase genes in the intestinal contents of grass carp provides insight into the release of major phosphorus from phytate in nature

Phytate is the most abundant organic phosphorus compound in nature, and microbial mineralization of phytate by phytase is a key process for phosphorus recycling in the biosphere. In the present study, beta-propeller phytase (BPP) gene fragments were readily amplified from the intestinal contents of grass carp (Ctenopharyngodon idellus) directly or from phytate-degrading isolates from the same source, confirming the widespread occurrence of BPP in aquatic communities. The amounts of sequences collected using these two methods differed (88 distinct genes versus 10 isolates), but the sequences showed the same general topology based on phylogenetic analysis. All of the sequences fell in five clusters and were distinct from those of Anabaena, Gloeobacter, Streptomyces, Flavobacterium, Prosthecochloris, and Desulfuromonas, which have never been found in the grass carp intestine. Analysis of the microbial diversity by denaturing gradient gel electrophoresis demonstrated that unculturable bacteria were dominant bacteria in the grass carp intestine and thus the predominant phytate-degrading organisms. The predominant cultured species corresponding to the phytate-degrading isolates, Pseudomonas, Bacillus and Shewanella species, might be the main source of known BPPs. A phytase from Brevundimonas was first obtained from cultured species. Combining our results with Lim et al.'s inference that phytate-mineralizing bacteria are widely distributed and highly diverse in nature (B. L. Lim, P. Yeung, C. Cheng, and J. E. Hill, ISME J. 1:321-330, 2007), we concluded that BPP is the major phytate-degrading enzyme in nature, that most of this enzyme might originate from unculturable bacteria, and that the distribution of BPP may be related to the type of niche. To our knowledge, this is the first study to experimentally estimate BPP diversity in situ.

Use of real-time PCR technique in studying rumen cellulolytic bacteria population as affected by level of roughage in swamp buffalo

A real-time polymerase chain reaction approach was used in this study to determine the population of major ruminal bacterial species (Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens) in digesta and rumen fluid of swamp buffalo (Bubalus bubalis). Four rumen-fistulated, male swamp buffalo were randomly assigned according to a 4 x 4 Latin square design to evaluate the effect of the urea-treated rice straw (roughage source)-to-concentrate ratio on cellulolytic bacterial distribution. Animals were fed roughage-to-concentrate (R:C) ratios of 100:0, 75:25, 50:50, and 25:75, respectively. At the end of each period, rumen fluid and digesta were collected at 0 h and 4 h post-morning-feeding. It was found that feeding urea-treated rice straw solely increased these three cellulolytic bacteria numbers up to 2.65 x 10(9) and 3.54 x 10(9) copies per milliliter for F. succinogenes, 5.10 x 10(7) and 7.40 x 10(7) copies per milliliter for R. flavefaciens, and 4.00 x 10(6) and 6.00 x 10(6) copies per milliliter for R. albus in rumen fluid and digesta, respectively. The distribution of the three cellulolytic bacteria species in digesta were highest at 3.21 x 10(9), 4.55 x 10(7), and 4.56 x 10(6) copies per milliliter for F. succinogenes, R. flavefaciens, and R. albus, respectively. Moreover, at 4 h post-morning-feeding, the populations of the three cellulolytic bacteria were higher than found at 0 h post-morning-feeding. It is most notable that F. succinogenes were the highest in population in the rumen of swamp buffalo and cellulolytic bacteria mostly adhered to feed digesta in the rumen.

A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene

The diversity of methanogenic Archaea from the gut of 6 humans was investigated by targeting mcrA, a molecular metabolic marker of methanogenesis. Three operational taxonomic units (OTUs) were recovered from about 400 clones analyzed, two of which were attributed to the expected Methanobacteriales Methanobrevibacter smithii (4 volunteers) and Methanosphaera stadtmanae (1 volunteer). The third OTU (1 volunteer) corresponded to a distant phylotype that does not cluster with any of the five methanogenic orders. This result, also supported by 16S archaeal sequences retrieved from the same volunteer, strongly suggests there may be a sixth order and hence potential underestimation of the role of methanogens in gut physiology.