Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge

Subacute rumen acidosis (SARA) occurs when highly fermentable carbohydrates are introduced into the diet, decreasing pH and disturbing the microbial ecology of the rumen. Rumen amylolytic bacteria rapidly catabolize starch, fermentation acids accumulate in the rumen and reduce environmental pH. Historically, antibiotics (e.g., monensin, MON) have been used in the prevention and treatment of SARA. Biochanin A (BCA), an isoflavone produced by red clover (Trifolium pratense), mitigates changes associated with starch fermentation ex vivo. The objective of the study was to determine the effect of BCA on amylolytic bacteria and rumen pH during a SARA challenge. Twelve rumen fistulated steers were assigned to 1 of 4 treatments: HF CON (high fiber control), SARA CON, MON (200 mg d^-1), or BCA (6 g d^-1). The basal diet consisted of corn silage and dried distiller’s grains ad libitum. The study consisted of a 2-wk adaptation, a 1-wk HF period, and an 8-d SARA challenge (d 1–4: 40% corn; d 5–8: 70% cracked corn). Samples for pH and enumeration were taken on the last day of each period (4 h). Amylolytic, cellulolytic, and amino acid/peptide-fermenting bacteria (APB) were enumerated. Enumeration data were normalized by log transformation and data were analyzed by repeated measures ANOVA using the MIXED procedure of SAS. The SARA challenge increased total amylolytics and APB, but decreased pH, cellulolytics, and in situ DMD of hay (P < 0.05). BCA treatment counteracted the pH, microbiological, and fermentative changes associated with SARA challenge (P < 0.05). Similar results were also observed with MON (P < 0.05). These results indicate that BCA may be an effective alternative to antibiotics for mitigating SARA in cattle production systems.

Ruminal cellulolytic bacteria abundance leads to the variation in fatty acids in the rumen digesta and meat of fattening lambs

Ruminal cellulolytic bacteria could be a diagnostic tool for determining the subacute rumen acidosis (SARA) risk in individual ruminants; however, a limited number of studies have investigated the effects of the abundance of ruminal cellulolytic bacteria on the fatty acid (FA) composition of the rumen digesta and the muscle of sheep. Thus, the objective of this study was to evaluate the effect of the variation of rumen cellulolytic bacteria on the rumen fermentation, rumen digesta, and muscle FA composition of fattening lambs fed an identical diet. Forty-eight lambs were reared in individual units and fed a high-concentrate diet consisting of 20% forage and 80% concentrate. All lambs were adapted to diets and facilities for 14 d, and sampling was for 63 d. At the end of the experiment, the rumen fluid, rumen digesta, and longissimus dorsi were collected after slaughter for the measurement of volatile fatty acids, ruminal bacterial DNA, rumen digesta, and muscle FAs. The lambs were classified into the lower cellulolytic bacteria (LCB, n = 10) group and the higher cellulolytic bacteria (HCB, n = 10) group according to the abundance of pH-sensitive cellulolytic bacteria (Ruminococcus albus, Ruminococcus flavefaciens, Fibrobacter succinogenes, and Butyrivibrio fibrisolvens) in the rumen. Ruminal acetate concentration was positively correlated with the number of R. flavefaciens, F. Succinogenes, and B. fibrisolvens (P < 0.05, r > 0.296), whereas propionate and valerate concentrations were negatively correlated with the amount of F. succinogenes and B. fibrisolvens (P < 0.05, r > 0.348). Compared with the LCB group, the acetate (P = 0.018) as well as acetate to propionate ratio (P = 0.012) in the HCB group was higher, but the valerate ratio was lower (P = 0.002). The proportions of even-chain FAs and odd- and branched-chain fatty acid in the rumen digesta of lambs with the HCB were higher (P < 0.05), while the polyunsaturated fatty acids decreased than those in the LCB lambs (P < 0.05), but those FA proportions in the meat were similar between the two groups. The proportion of C17:0 in the meat of lambs in the HCB group was lower than that of lambs in the LCB group (P = 0.033). The proportions of conjugated linoleic acid in rumen digesta and meat were both higher in the HCB group than that in the LCB group (P = 0.046). These results indicated that the ruminal cellulolytic bacteria can alter the FA compositions in rumen digesta and further influenced the FA compositions in the meat of sheep.

Gut microbiota health closely associates with PCB153-derived risk of host diseases

Although the production and use of PCB153 have been banned globally, PCB153 pollution remains because of its persistence and long half-life in the environment. There is ongoing evidence that exposure to PCB153 may influence gut microbiota health and increase the risk of host health. It is needed to illuminate whether there are associations between gut microbiota dysregulation and PCB153-induced host diseases. Importantly, it is urgently needed to find specific strains as biomarkers to monitor PCB153 pollution and associated disorders. The work aims to investigate the change of gut microbiota composition, structure and diversity and various host physiological indexes, to ravel the chain causality of PCB153, gut microbiota health and host health, and to find potential gut microbiota markers for PCB153 pollution. Here, adult female mice were administrated with PCB153. Obtained results indicated that PCB153 led to gut microbiota health deterioration. PCB153 exposure also induced obesity, hepatic lipid accumulation, abdominal adipose tissue depots and dyslipidemia in mice. Furthermore, specific gut microbiota significantly correlated with the host health indexes. This work provides support for the relationship between gut microbiota aberrance derived from PCB153 and risk of host health, and offers some indications of possible indicative functions of gut microbiota on PCB153 pollution.

The impact of therapeutic-dose induced intestinal enrofloxacin concentrations in healthy pigs on fecal Escherichia coli populations

BACKGROUND

Knowledge of therapy-induced intestinal tract concentrations of antimicrobials allows for interpretation and prediction of antimicrobial resistance selection within the intestinal microbiota. This study describes the impact of three different doses of enrofloxacin (ENR) and two different administration routes on the intestinal concentration of ENR and on the fecal Escherichia coli populations in pigs. Enrofloxacin was administered on three consecutive days to four different treatment groups. The groups either received an oral bolus administration of ENR (conventional or half dose) or an intramuscular administration (conventional or double dose).

RESULTS

Quantitative analysis of fecal samples showed high ENR concentrations in all groups, ranging from 5.114 ± 1.272 μg/g up to 39.54 ± 10.43 μg/g at the end of the treatment period. In addition, analysis of the luminal intestinal content revealed an increase of ENR concentration from the proximal to the distal intestinal tract segments, with no significant effect of administration route. Fecal samples were also screened for resistance in E. coli isolates against ENR. Wild-type (MIC≤0.125 μg/mL) and non-wild-type (0.125 < MIC≤2 μg/mL) E. coli isolates were found at time 0 h. At the end of treatment (3 days) only non-wild-type isolates (MIC≥32 μg/mL) were found.

CONCLUSIONS

In conclusion, the observed intestinal ENR concentrations in all groups showed to be both theoretically (based on pharmacokinetic and pharmacodynamic principles) and effectively (in vivo measurement) capable of significantly reducing the intestinal E. coli wild-type population.

Xpert MTB/RIF and Xpert MTB/RIF Ultra assays for active tuberculosis and rifampicin resistance in children

BACKGROUND

Every year, at least one million children become ill with tuberculosis and around 200,000 children die. Xpert MTB/RIF and Xpert Ultra are World Health Organization (WHO)-recommended rapid molecular tests that simultaneously detect tuberculosis and rifampicin resistance in adults and children with signs and symptoms of tuberculosis, at lower health system levels. To inform updated WHO guidelines on molecular assays, we performed a systematic review on the diagnostic accuracy of these tests in children presumed to have active tuberculosis.

OBJECTIVES

Primary objectives • To determine the diagnostic accuracy of Xpert MTB/RIF and Xpert Ultra for (a) pulmonary tuberculosis in children presumed to have tuberculosis; (b) tuberculous meningitis in children presumed to have tuberculosis; (c) lymph node tuberculosis in children presumed to have tuberculosis; and (d) rifampicin resistance in children presumed to have tuberculosis - For tuberculosis detection, index tests were used as the initial test, replacing standard practice (i.e. smear microscopy or culture) - For detection of rifampicin resistance, index tests replaced culture-based drug susceptibility testing as the initial test Secondary objectives • To compare the accuracy of Xpert MTB/RIF and Xpert Ultra for each of the four target conditions • To investigate potential sources of heterogeneity in accuracy estimates - For tuberculosis detection, we considered age, disease severity, smear-test status, HIV status, clinical setting, specimen type, high tuberculosis burden, and high tuberculosis/HIV burden - For detection of rifampicin resistance, we considered multi-drug-resistant tuberculosis burden • To compare multiple Xpert MTB/RIF or Xpert Ultra results (repeated testing) with the initial Xpert MTB/RIF or Xpert Ultra result SEARCH METHODS: We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), Scopus, the WHO International Clinical Trials Registry Platform, ClinicalTrials.gov, and the International Standard Randomized Controlled Trials Number (ISRCTN) Registry up to 29 April 2019, without language restrictions.

SELECTION CRITERIA

Randomized trials, cross-sectional trials, and cohort studies evaluating Xpert MTB/RIF or Xpert Ultra in HIV-positive and HIV-negative children younger than 15 years. Reference standards comprised culture or a composite reference standard for tuberculosis and drug susceptibility testing or MTBDRplus (molecular assay for detection of Mycobacterium tuberculosis and drug resistance) for rifampicin resistance. We included studies evaluating sputum, gastric aspirate, stool, nasopharyngeal or bronchial lavage specimens (pulmonary tuberculosis), cerebrospinal fluid (tuberculous meningitis), fine needle aspirates, or surgical biopsy tissue (lymph node tuberculosis).

DATA COLLECTION AND ANALYSIS

Two review authors independently extracted data and assessed study quality using the Quality Assessment of Studies of Diagnostic Accuracy - Revised (QUADAS-2). For each target condition, we used the bivariate model to estimate pooled sensitivity and specificity with 95% confidence intervals (CIs). We stratified all analyses by type of reference standard. We assessed certainty of evidence using the GRADE approach.

MAIN RESULTS

For pulmonary tuberculosis, 299 data sets (68,544 participants) were available for analysis; for tuberculous meningitis, 10 data sets (423 participants) were available; for lymph node tuberculosis, 10 data sets (318 participants) were available; and for rifampicin resistance, 14 data sets (326 participants) were available. Thirty-nine studies (80%) took place in countries with high tuberculosis burden. Risk of bias was low except for the reference standard domain, for which risk of bias was unclear because many studies collected only one specimen for culture. Detection of pulmonary tuberculosis For sputum specimens, Xpert MTB/RIF pooled sensitivity (95% CI) and specificity (95% CI) verified by culture were 64.6% (55.3% to 72.9%) (23 studies, 493 participants; moderate-certainty evidence) and 99.0% (98.1% to 99.5%) (23 studies, 6119 participants; moderate-certainty evidence). For other specimen types (nasopharyngeal aspirate, 4 studies; gastric aspirate, 14 studies; stool, 11 studies), Xpert MTB/RIF pooled sensitivity ranged between 45.7% and 73.0%, and pooled specificity ranged between 98.1% and 99.6%. For sputum specimens, Xpert Ultra pooled sensitivity (95% CI) and specificity (95% CI) verified by culture were 72.8% (64.7% to 79.6%) (3 studies, 136 participants; low-certainty evidence) and 97.5% (95.8% to 98.5%) (3 studies, 551 participants; high-certainty evidence). For nasopharyngeal specimens, Xpert Ultra sensitivity (95% CI) and specificity (95% CI) were 45.7% (28.9% to 63.3%) and 97.5% (93.7% to 99.3%) (1 study, 195 participants). For all specimen types, Xpert MTB/RIF and Xpert Ultra sensitivity were lower against a composite reference standard than against culture. Detection of tuberculous meningitis For cerebrospinal fluid, Xpert MTB/RIF pooled sensitivity and specificity, verified by culture, were 54.0% (95% CI 27.8% to 78.2%) (6 studies, 28 participants; very low-certainty evidence) and 93.8% (95% CI 84.5% to 97.6%) (6 studies, 213 participants; low-certainty evidence). Detection of lymph node tuberculosis For lymph node aspirates or biopsies, Xpert MTB/RIF pooled sensitivity and specificity, verified by culture, were 90.4% (95% CI 55.7% to 98.6%) (6 studies, 68 participants; very low-certainty evidence) and 89.8% (95% CI 71.5% to 96.8%) (6 studies, 142 participants; low-certainty evidence). Detection of rifampicin resistance Xpert MTB/RIF pooled sensitivity and specificity were 90.0% (67.6% to 97.5%) (6 studies, 20 participants; low-certainty evidence) and 98.3% (87.7% to 99.8%) (6 studies, 203 participants; moderate-certainty evidence).

AUTHORS' CONCLUSIONS

We found Xpert MTB/RIF sensitivity to vary by specimen type, with gastric aspirate specimens having the highest sensitivity followed by sputum and stool, and nasopharyngeal specimens the lowest; specificity in all specimens was > 98%. Compared with Xpert MTB/RIF, Xpert Ultra sensitivity in sputum was higher and specificity slightly lower. Xpert MTB/RIF was accurate for detection of rifampicin resistance. Xpert MTB/RIF was sensitive for diagnosing lymph node tuberculosis. For children with presumed tuberculous meningitis, treatment decisions should be based on the entirety of clinical information and treatment should not be withheld based solely on an Xpert MTB/RIF result. The small numbers of studies and participants, particularly for Xpert Ultra, limits our confidence in the precision of these estimates.

Soybean oligosaccharide, stachyose, and raffinose in broilers diets: effects on odor compound concentration and microbiota in cecal digesta

Soybean oligosaccharides have been previously shown to be associated with the production of major odor-causing compounds in broilers, although little is known about the role of stachyose and raffinose, which are key components of soybean oligosaccharide, in broiler cecal microbiota and odor compound production. To this end, soybean oligosaccharide, stachyose, and raffinose were added to the birds' diets to investigate their effects on odor compound production and the microbial community characteristics of the cecum in broilers. A total of 300 one-day-old Arbor Acre broilers with similar initial live weight were randomly allocated into 5 dietary groups with 6 replicates of 10 birds. The diets included soybean meal (positive control), soybean meal-free (negative control), 0.6% soybean oligosaccharide, 0.6% stachyose, or 0.6% raffinose. After a 49-D feeding period, both ceca were aseptically removed postmortem, and the contents were collected and analyzed for skatole, indole, volatile fatty acids, and lactic acid by using high performance liquid chromatography. Bacterial communities were detected by using a high-throughput sequencing platform based on IlluminaMiSeq 2500. Levels of skatole and indole tended to be lower in the dietary supplementation of oligosaccharides. The lowest levels of skatole and indole were observed in the stachyose group (P < 0.05), while the highest levels were found in the negative control group (P < 0.05). Concentrations of acetic acid and propionic acid in the stachyose group were increased (P < 0.05) while those of butyric acid and lactic acid were decreased (P < 0.05) compared with the soybean oligosaccharide and raffinose groups. Firmicutes and Bacteroidetes were prevalent in all groups, the proportion of Bacteroidetes was slightly decreased in the stachyose group, and Verrucomicrobia was abundant in the raffinose group (P > 0.05). Bacterial genera Alistipes and Parabacteroides were comparably abundant in the stachyose group, while Bacteroides, Lactobacillus, and Akkermansia were more abundant in the negative control, stachyose, and raffinose groups, respectively. Collectively, these findings demonstrated that dietary oligosaccharide supplementation significantly reduced odor compound production by modulating the cecal microbial community. Compared with soybean oligosaccharide and raffinose, the addition of stachyose into diets may help improve gut fermentation and minimize odor compound generation in broilers.

Topical Application of Adult Cecal Contents to Eggs Transplants Spore-Forming Microbiota but Not Other Members of the Microbiota to Chicks

The intestinal microbiota plays an essential role in the metabolism and immune competence of chickens from the first day after hatching. In modern production systems, chicks are isolated from adult chickens, instead hatching in a clean environment. As a result, chicks are colonized by environmental bacteria, including potential pathogens. There is a need to investigate methods by which chicks can be exposed to a more appropriate microbial community at hatching. Such methods must be easy to apply in a hatchery and produce consistent results. The development of the intestinal microbiota of chicks hatched from eggs sprayed with dilute adult cecal content during incubation was observed at 0, 3, 7, and 14 days posthatching (dph) across two experiments. High-throughput Illumina sequencing was performed for the V4 hypervariable region of the 16S rRNA gene. A topical treatment of dilute adult cecal content was sufficient to transplant spore-forming bacteria such as Lachnospiraceae and Ruminococcaceae However, this treatment was not able to transplant other taxa that are considered to be core elements of the chicken cecal microbiota, such as Bacteroidaceae, Lactobacillaceae, Bifidobacteriaceae, and Burkholderiaceae The topical treatment significantly altered the microbiota of chicks immediately posthatching and accelerated the normal development of the microbiota with earlier colonization by Ruminococcaceae in the cecum and "Candidatus Arthromitus" in the ileum. The effect of the treatment on the cecal microbiota was maximal at 3 dph but diminished over time.IMPORTANCE Over the last 60 years poultry production has intensified in response to increased demand for meat. In modern systems, chicks hatch without contacting chickens and their gut bacteria. Consequently, they are colonized by environmental bacteria that may cause disease. The normal bacteria that live in the gut, or intestinal microbiota, play an important role in the development of the immune system. Therefore, it is essential to find easy ways to expose chicks to the more appropriate bacteria at hatching. This experiment investigated whether spraying eggs with adult cecal contents was sufficient to transfer an adult microbiota to chicks. Our findings show that spore-forming bacteria were transplanted, but other members of the microbiota were not. In this respect, the spray application was partially successful, but the timing of the spray needs to be modified to ensure that more bacteria are transferred.

Hysterical tetracycline in intensive poultry farms accountable for substantial gene resistance, health and ecological risk in Egypt- manure and fish

Although the poultry production sector plays a key role in sustaining the majority of animal protein demand in Egypt, the deleterious effects of widespread antibiotic resistance on health and environment are currently not well recognized. Litter and dropping samples from broiler and layer poultry farms as well as, tilapia samples from the Nile River and aquaculture farms were collected from Upper Egypt. Samples were extracted and examined for tetracycline residues [tetracycline (TC), chlortetracycline (CTC), oxytetracycline (OTC) and doxycycline (DC)] using HPLC. In addition, tetracycline resistance genes [tet (M), tet (W), tet (Q) and tet (G)] were screened from pooled intestinal contents collected from twelve broiler farms in Upper Egypt. The antibiotic resistance genes results revealed that tet (W) was confirmed to be expressed in all intestinal samples. In contrast, tet (Q) and tet (M) were detected only in 42% and 17% of the samples, respectively. CTC and OTC were the antimicrobial compounds with the highest concentrations in poultry litter and droppings, with concentrations of 6.05 and 2.47 μg g^-1 (CTC) and 5.9 and 1.33 μg g^-1 (OTC), respectively. However, the concentrations of DC were significantly higher than those of the other compounds in both aquaculture and Nile River tilapia. The tetracycline residue levels in aquaculture tilapia were significantly higher than those in Nile River tilapia. The hazard quotients (HQs) exceeded 1 for OTC, CTC and DC, which highlights the great risk of using broiler litter to fertilize agricultural land. Moreover, the presence of DC and CTC indicates that consumption of aquaculture tilapia poses a considerable health risk. Therefore, poultry litter or droppings containing tetracycline residues and tet resistance determinants used for aquaculture or as farmland fertilizers could be major sources of antibiotic resistance in fish, humans and environment.

Maternal Dietary Protein Intake Influences Milk and Offspring Gut Microbial Diversity in a Rat (Rattus norvegicus) Model

Historically, investigators have assumed microorganisms identified in mother’s milk to be contaminants, but recent data suggest that milk microbiota may contribute to beneficial maternal effects. Microorganisms that colonize the gastrointestinal tracts of newborn mammals are derived, at least in part, from the maternal microbial population. Milk-derived microbiota is an important source of this microbial inocula and we hypothesized that the maternal diet contributes to variation in this microbial community. To evaluate the relationship between a mother’s diet and milk microbiome, we fed female rats a low- or high-protein diet and mated all individuals. Milk and cecal contents were collected from dams at peak lactation (14-day post-partum), and the bacterial composition of each community was assessed by 16S rRNA gene amplicon sequencing. Our findings revealed higher dietary protein intake decreased fecal microbial diversity but increased milk microbial and pup cecum diversity. Further, the higher dietary protein intake resulted in a greater abundance of potentially health-promoting bacteria, such as Lactobacillus spp. These data suggest that dietary protein levels contribute to significant shifts in the composition of maternal milk microbiota and that the functional consequences of these changes in microbial inocula might be biologically important and should be further explored.

Changes in Ileal Microbial Composition and Microbial Metabolism by an Early-Life Galacto-Oligosaccharides Intervention in a Neonatal Porcine Model

Galacto-oligosaccharides (GOS), functional oligosaccharides with natural characteristics, are important active substances in milk that play an important role in the development of intestinal microbiota and the immune system of newborns. The intestinal maturation of piglets resembles that of human newborns and infants. Therefore, we used the newborn piglet model to study the effects of early-life GOS intervention. Six litters of neonatal piglets (10 piglets per litter) with the same average birth weight were divided into control (CON) and GOS (GOS) groups in each litter. Piglets in the GOS group were given 10 mL of GOS solution daily during the first week after birth, while piglets in the CON group were given the same dose of physiological saline orally. One pig per group from each litter was euthanized on day 8 and day 21. Results revealed that ileal microbiota composition was significantly enriched in Lactobacillus and unclassified Lactobacillaceae, and reduced in Clostridium sensu stricto on day 8 and day 21 after GOS intervention. Additionally, Escherichia significantly decreased on day 21 following the early-life GOS intervention. Moreover, the content of microbial metabolites, endocrine peptides, and the mRNA expression of anti-inflammatory cytokines and antimicrobial peptides increased in the GOS group. These findings provide guidelines for early prebiotic supplementation for lactating newborns.

Stomach contents of the archaeocete Basilosaurus isis: Apex predator in oceans of the late Eocene

Apex predators live at the top of an ecological pyramid, preying on animals in the pyramid below and normally immune from predation themselves. Apex predators are often, but not always, the largest animals of their kind. The living killer whale Orcinus orca is an apex predator in modern world oceans. Here we focus on an earlier apex predator, the late Eocene archaeocete Basilosaurus isis from Wadi Al Hitan in Egypt, and show from stomach contents that it fed on smaller whales (juvenile Dorudon atrox) and large fishes (Pycnodus mokattamensis). Our observations, the first direct evidence of diet in Basilosaurus isis, confirm a predator-prey relationship of the two most frequently found fossil whales in Wadi Al-Hitan, B. isis and D. atrox. This extends our understanding of their paleoecology. Late Eocene Basilosaurus isis, late Miocene Livyatan melvillei, and modern Orcinus orca are three marine apex predators known from relatively short intervals of time. Little is known about whales as apex predators through much of the Cenozoic era, and whales as apex predators deserve more attention than they have received.

Effects of dietary rapeseed meal supplementation on cecal microbiota in laying hens with different flavin-containing monooxygenase 3 genotypes

To evaluate the effect of dietary rapeseed meal (RM) supplementation on cecal trimethylamine and bacteria in laying hens with different flavin-containing monooxygenase 3 (FMO3) genotypes, a 3 × 2 2-factorial arrangement was employed using FMO3 genotypes (AA, AT, and TT) and dietary RM (0 and 14% of diet) as the main effects. At 50 wk of age, 36 hens of AT genotype and 36 hens of TT genotype were randomly allotted to one of the 2 dietary treatments, and each dietary treatment consisted of 3 replicates with 6 birds each. A total of 12 hens with AA genotype were allotted to one of the 2 dietary treatments that consisted of 3 replicates with 2 hens. Hens were fed 0% RM in a corn-soybean (SM) diet for one wk before the 6-week feeding trial period. Dietary RM supplementation increased trimethylamine (TMA) concentrations in both egg yolks (P < 0.0001) and cecal chyme (P < 0.0001). Dietary RM supplementation increased bacterial abundance and diversity (P < 0.0001). Weighted UniFrac, Nonmetric Multidimensional Scaling, and analysis of similarity (R-ANOSIM = 0.1516; P-value = 0.014) indicated distinct clustering was dependent on diets rather than FMO3 genotypes. Twenty-four phyla (most dominant, Bacteroides, Firmicutes, and Proteobacteria) and 229 genera were identified in the cecal samples. Compared with the SM diets, RM diets increased the proportion of Firmicutes (P = 0.004), Proteobacteria (P = 0.006), and Firmicutes:Bacteroides (P = 0.001), and some low-abundance phyla (P < 0.01), whereas the abundance of Bacteroides was lower (P = 0.0002). The abundance of 42 genera varied with dietary types. Six phyla and 35 genera were positively correlated with TMA concentration in the cecal chyme. In conclusion, the major TMA-producing bacteria in cecal were from Firmicutes and Proteobacteria phyla. The major TMA-producing bacterial genera could be from the genera that positively correlated with TMA concentration.

In vitro effects of inulin and soya bean oligosaccharide on skatole production and the intestinal microbiota in broilers

The experiment was conducted to investigate the in vitro effects of inulin and soya bean oligosaccharide (SBO) on the metabolism of L-tryptophan (L-try) to skatole production, and the intestinal microbiota in broilers. Treatments were as follows: caecal microbiota control (Cc), Cc + inulin, Cc + SBO, rectal microbiota control (Rc), Rc + inulin and Rc + SBO. Microbial suspensions were anaerobically incubated at 38°C for 24 hr. The results showed that concentrations of skatole and acetic acid were significantly lower in caecal microbiota fermentation broth (MFB) than those in rectal MFB (p < .05). Addition of inulin or SBO significantly decreased the concentrations of indole and skatole and rate of L-try degradation (p < .05). Inulin groups had lower indole than SBO groups (p < .05). PCR-DGGE analysis revealed that addition of inulin or SBO decreased the microbiota richness (p < .05), but no significant differences in Shannon index (p > .05). Four distinct bands were detected in inulin and SBO groups, which were related to two of Bacteroides, one of Firmicutes and Bifidobacteria. Six bands were detected only in control groups, which represented uncultured Rikenellaceae, Roseburia, Escherichia/Shigella dysenteriae, Bacteroides uniformis (T), Parabacteroides distasonis and Enterobacter aerogenes. Populations of Lactobacilli, Bifidobacteria and total bacteria in inulin groups were higher than those in control groups (p < .05). For SBO groups, only population of total bacteria increased (p < .05). However, there were no significant differences in Escherichia coli population among treatments (p > .05). These results suggest that reduced concentrations of skatole and indole in the presence of inulin and SBO may be caused by decrease in L-try degradation rate, which were caused by change in microbial ecosystem and pH value. Uncultured B. uniformis (T) and E. aerogenes may be responsible for degradation of L-try to skatole.

Time course of Salmonella shedding and antibody response in naturally infected pigs during grower-finisher stage

A longitudinal trial was conducted to determine the course of Salmonella shedding and antibody response in naturally infected grower-finisher pigs. Ten-week-old pigs (n = 45) were transferred from a farm with history of salmonellosis and housed at a research facility. Weekly fecal samples (weeks 1 to 11) as well as tissue samples at slaughter were cultured for Salmonella. Serum samples were tested for presence of Salmonella antibody by enzyme-linked immunosorbent assay (ELISA). Data were analyzed using a multilevel mixed-effects logistic regression model. Over 10 wk, 91% and 9% of pigs shed Salmonella ≤ 4 and > 5 times, respectively. The estimated median of Salmonella shedding duration was 3 to 4 wk but some pigs shed Salmonella for up to 8 wk. Salmonella shedding increased 1 wk post-arrival but followed a decreasing pattern afterwards up to week 11 (P < 0.05). Salmonella isolates (n = 29), which were recovered from 18 pigs at different occasions, were S. Typhimurium (28%), S. Livingstone (21%), S. Infantis (14%), S. Montevideo (7%), S. Benfica (3%), S. Amsterdam (3%), S. Senftenberg (17%), and S. I:Rough-O (7%). Of 11 pigs from which the first and last isolates were serotyped, 10 pigs were reinfected with a different serotype. At slaughter, Salmonella was isolated from 7 pigs, of which 5 (71%) had not tested positive for at least 7 wk prior to slaughter. Antibody response peaked 4 wk after the peak of Salmonella infection; Salmonella shedding reduced as antibody response elevated (P < 0.05). These findings indicate that pigs may shed Salmonella into the mid-point of the grower-finisher stage and may be reinfected with different serotypes.

Administration of Inulin-Supplemented Gluten-Free Diet Modified Calcium Absorption and Caecal Microbiota in Rats in a Calcium-Dependent Manner

In coeliac disease (CD), the risk of adverse calcium balance and reduced bone density is induced mainly by the disease, but also by a gluten-free diet (GFD), the only accepted CD therapy. Prebiotics through the beneficial impact on intestinal microbiota may stimulate calcium (Ca) absorption. In the present study, we hypothesised that the dietary inulin in GFD would influence positively the intestinal microbiota, and by that will stimulate the absorption of calcium (Ca), especially in the conditions of Ca malnutrition. In a six-weeks nutritional experiment on growing a significant (p < 0.05) luminal acidification, decrease in ammonia concentration and stimulation of short chain fatty acids formation indicated inulin-mediated beneficial effects on the caecal microbiota. However, the effect of inulin on characteristics of intestinal microbiota and mineral utilization depended on the dietary Ca intake from GFDs. Inulin stimulated bifidobacteria, in particular B. animalis species, only if a recommended amount of Ca was provided. Most benefits to mineral utilization from inulin consumption were seen in rats fed Ca-restricted GFD where it increased the relative Ca absorption. Administration of inulin to a GFDs could be a promising dietary strategy for beneficial modulation of intestinal ecosystem and by that for the improvement the Ca absorption.

Lactobacillus colini sp. nov., isolated from Northern Bobwhite (Colinus virginianus)

Biochemical and molecular studies were performed on five unknown bacterial strains isolated from the intestinal contents of Northern Bobwhites (Colinus virginianus) collected from western Texas, USA. The strains were Gram-stain-positive, catalase-negative, non-spore-forming rods arranged in single cells, pairs or short chains. Colonies on Columbia blood agar are circular, flat, entire, approximately 0.5-1.5 mm in diameter and surrounded with a zone of alpha-haemolysis at after incubation for 48 h at 37 °C. Colonies on MRS agar are umbonate with irregular edge, opaque and approximately 1-1.5 mm in diameter after incubation for 48 h. The 16S rRNA gene sequences of the isolates were identical and the highest sequence similarity (97 %) was found to the type strains of Lactobacillus gasseri, L. johnsonii and L. taiwanensis. The strains were distinguishable from related species of the genus Lactobacilluson the basis of carbohydrate fermentation, enzymatic production and fatty acid profiles. The peptidoglycan type is l-Lys-d-Asp (A4α). The DNA G+C content is 35.6 mol%. Major cellular fatty acids are C14 : 0, C16 : 0 and C18 : 1 ω9c. Based on phenotypic, phylogenetic and chemotaxonomic information, the strains represent a novel species of the genus Lactobacillus for which the name Lactobacillus colini sp. nov. is proposed. The type strain is 111144 L1T (=DSM 101872T=KCTC 21086T).

Modulatory effects of condensed tannin fractions of different molecular weights from a Leucaena leucocephala hybrid on the bovine rumen bacterial community in vitro

BACKGROUND

Condensed tannin (CT) fractions of different molecular weights (MWs) may affect rumen microbial metabolism by altering bacterial diversity. In this study the effects of unfractionated CTs (F0) and five CT fractions (F1-F5) of different MWs (F1, 1265.8 Da; F2, 1028.6 Da; F3, 652.2 Da; F4, 562.2 Da; F5, 469.6 Da) from Leucaena leucocephala hybrid-Rendang (LLR) on the structure and diversity of the rumen bacterial community were investigated in vitro.

RESULTS

Real-time polymerase chain reaction assay showed that the total bacterial population was not significantly (P > 0.05) different among the dietary treatments. Inclusion of higher-MW CT fractions F1 and F2 significantly (P < 0.05) increased the Fibrobacter succinogenes population compared with F0 and CT fractions F3-F5. Although inclusion of F0 and CT fractions (F1-F5) significantly (P < 0.05) decreased the Ruminococcus flavefaciens population, there was no effect on the Ruminococcus albus population when compared with the control (without CTs). High-throughput sequencing of the V3 region of 16S rRNA showed that the relative abundance of genera Prevotella and unclassified Clostridiales was significantly (P < 0.05) decreased, corresponding with increasing MW of CT fractions, whereas cellulolytic bacteria of the genus Fibrobacter were significantly (P < 0.05) increased. Inclusion of higher-MW CT fractions F1 and/or F2 decreased the relative abundance of minor genera such as Ruminococcus, Streptococcus, Clostridium XIVa and Anaeroplasma but increased the relative abundance of Acinetobacter, Treponema, Selenomonas, Succiniclasticum and unclassified Spirochaetales compared with the control and lower-MW CT fractions.

CONCLUSION

This study indicates that CT fractions of different MWs may play an important role in altering the structure and diversity of the rumen bacterial community in vitro, and the impact was more pronounced for CT fractions with higher MW. © 2016 Society of Chemical Industry.

Effect of dietary protein sources on the small intestine microbiome of weaned piglets based on high-throughput sequencing

In this study, we comprehensively investigated the effect of dietary protein sources on the gut microbiome of weaned piglets with diets comprising different protein source using High-throughput 16SrRNA gene-based Illumina Miseq. A total of 48 healthy weaned piglets were allocated randomly to four treatments with 12 piglets in each group. The weaned piglets were fed with diets containing soybean meal (SBM), cottonseed meal (CSM), SBM and CSM (SC) or fish meal (FM). The intestinal content samples were taken from five segments of the small intestine. DNA was extracted from the samples and the V3-V4 regions of the 16SrRNA gene were amplified. The microbiota of the contents of the small intestine were very complex, including more than 4000 operational taxonomic units belonging to 32 different phyla. Four bacterial populations (i.e. Firmicutes, Proteobacteria, Bacteroidetes and Acidobacteria) were the most abundant bacterial groups. The genera Lactobacillus and Clostridium were found in slightly higher proportions in the groups with added CSM compared to the other groups. The proportion of reads assigned to the genus Escherichia/Shigella was much higher in the FM group. In conclusion, dietary protein source had significant effects on the small microbiome of weaned piglets.

SIGNIFICANCE AND IMPACT OF THE STUDY

Dietary protein source have the potential to affect the small intestine microbiome of weaned piglets that will have a large impact on its metabolic capabilities and intestinal health. In this study, we successfully identified the microbiomes in the contents of the small intestine in the weaned piglets that were fed different protein source diets using high-throughput sequencing. The finding provided an evidence for the option of the appropriate protein source in the actual production.

The short-chain fatty acid receptor, FFA2, contributes to gestational glucose homeostasis

The structure of the human gastrointestinal microbiota can change during pregnancy, which may influence gestational metabolism; however, a mechanism of action remains unclear. Here we observed that in wild-type (WT) mice the relative abundance of Actinobacteria and Bacteroidetes increased during pregnancy. Along with these changes, short-chain fatty acids (SCFAs), which are mainly produced through gut microbiota fermentation, significantly changed in both the cecum and peripheral blood throughout gestation in these mice. SCFAs are recognized by G protein-coupled receptors (GPCRs) such as free fatty acid receptor-2 (FFA2), and we have previously demonstrated that the fatty acid receptor-2 gene (Ffar2) expression is higher in pancreatic islets during pregnancy. Using female Ffar2-/- mice, we explored the physiological relevance of signaling through this GPCR and found that Ffar2-deficient female mice developed fasting hyperglycemia and impaired glucose tolerance in the setting of impaired insulin secretion compared with WT mice during, but not before, pregnancy. Insulin tolerance tests were similar in Ffar2-/- and WT mice before and during pregnancy. Next, we examined the role of FFA2 in gestational β-cell mass, observing that Ffar2-/- mice had diminished gestational expansion of β-cells during pregnancy. Interestingly, mouse genotype had no significant impact on the composition of the gut microbiome, but did affect the observed SCFA profiles, suggesting a functional difference in the microbiota. Together, these results suggest a potential link between increased Ffar2 expression in islets and the alteration of circulating SCFA levels, possibly explaining how changes in the gut microbiome contribute to gestational glucose homeostasis.

Evaluation of Xpert® MTB/RIF Assay in Induced Sputum and Gastric Lavage Samples from Young Children with Suspected Tuberculosis from the MVA85A TB Vaccine Trial

Objective

Diagnosis of childhood tuberculosis is limited by the paucibacillary respiratory samples obtained from young children with pulmonary disease. We aimed to compare accuracy of the Xpert^® MTB/RIF assay, an automated nucleic acid amplification test, between induced sputum and gastric lavage samples from young children in a tuberculosis endemic setting.

Methods

We analyzed standardized diagnostic data from HIV negative children younger than four years of age who were investigated for tuberculosis disease near Cape Town, South Africa [2009–2012]. Two paired, consecutive induced sputa and early morning gastric lavage samples were obtained from children with suspected tuberculosis. Samples underwent Mycobacterial Growth Indicator Tube [MGIT] culture and Xpert MTB/RIF assay. We compared diagnostic yield across samples using the two-sample test of proportions and McNemar’s χ² test; and Wilson’s score method to calculate sensitivity and specificity.

Results

1,020 children were evaluated for tuberculosis during 1,214 admission episodes. Not all children had 4 samples collected. 57 of 4,463[1.3%] and 26 of 4,606[0.6%] samples tested positive for Mycobacterium tuberculosis on MGIT culture and Xpert MTB/RIF assay respectively. 27 of 2,198[1.2%] and 40 of 2,183[1.8%] samples tested positive [on either Xpert MTB/RIF assay or MGIT culture] on induced sputum and gastric lavage samples, respectively. 19/1,028[1.8%] and 33/1,017[3.2%] admission episodes yielded a positive MGIT culture or Xpert MTB/RIF assay from induced sputum and gastric lavage, respectively. Sensitivity of Xpert MTB/RIF assay was 8/30[26.7%; 95% CI: 14.2–44.4] for two induced sputum samples and 7/31[22.6%; 11.4–39.8] [p = 0.711] for two gastric lavage samples. Corresponding specificity was 893/893[100%;99.6–100] and 885/890[99.4%;98.7–99.8] respectively [p = 0.025].

Conclusion

Sensitivity of Xpert MTB/RIF assay was low, compared to MGIT culture, but diagnostic performance of Xpert MTB/RIF did not differ sufficiently between induced sputum and gastric lavage to justify selection of one sampling method over the other, in young children with suspected pulmonary TB.

Trial Registration

ClinicalTrials.gov NCT00953927

Comparison of fluorescence microscopy and Ziehl-Neelsen technique in diagnosis of tuberculosis in paediatric patients

Early diagnosis of tuberculosis is very important for therapeutic reasons and to control the spread of infection. The purpose of this study was to compare the efficacy of fluorescence (FL) microscopy in comparison to Ziehl-Neelsen (ZN) staining. A total of 103 samples were collected from paediatric tuberculosis (TB) suspects and processed using Petroff's method. The smears were subjected to ZN and FL staining for the detection of acid-fast bacilli (AFB). Positive smears were graded according to scale of International Union Against Tuberculosis and Lung Disease and World Health Organisation (IUATLD/WHO). Out of 103 pulmonary and extra-pulmonary samples, 7(6.8%) were positive for AFB on the ZN method, while the positivity increased to 9(8.7%) on the FL method. Two positive samples were missed on ZN staining which were found to be positive with FL microscopy; thus overall positivity increased by 2/9 (22.22%) by FL microscopy over the conventional ZN method. The difference in case detection was found to be statistically significant (p<0.00). FL technique has a better diagnostic value and is less time-consuming compared to ZN in diagnosing tuberculosis in paediatric patients.

[The determination of stomach contents left on the material objects and in the environment]

The objective of the present experimental study was to develop the qualitatively new method for the determination of stomach contents left on the material objects and in the environment with special reference to the cases of aspiration asphyxia. We proposed the original approach for the determination of the origin of the traces of stomach contents based on the detection of pepsin, an enzyme that digests in the acidic milieu protein substances, such as gelatin (hydrolyzed collagen), a component of the emulsion layer of X-ray and photographic films. Samples of the stomach contents were taken from a corpse and placed on the surface of various materials that did not absorb moisture or repulsed it. In addition, materials undergoing putrefactive decomposition were investigated. Moreover, stains left by the cadaveric lung sections from the subjects who allegedly died from aspiration asphyxia on the emulsion layers were studied. A specially developed method was employed to detect pepsin, the main enzyme of the gastric juice. The majority of the studied samples including the control ones exhibited pepsin activity. The results of the study suggest the possibility of application of the proposed method for the detection of stomach contents on the environmental objects provided the material being studied avoided putrefactive modification.

Characteristics of fluid composition of left displaced abomasum in beef cattle fed high-starch diets

To clarify the pathophysiology of left displaced abomasum (LDA), beef cattle fed high-starch diets were examined. The abomasal pH in beef cattle with LDA was lower than that in non-LDA reference animals (data from beef cattle at an abattoir), suggesting that it facilitated acidity. Bacteriological examinations of the abomasal fluid in cattle with LDA revealed the presence of Pseudomonas spp., Clostridium spp. and Candida spp., presumably reflecting the accelerated influx of ruminal fluid into the abomasum. Biochemical analyses of serum revealed that LDA cattle had higher lactic acid and lower vitamin A and E levels than non-LDA reference animals. These results indicate that beef cattle with LDA may suffer from vitamin A and E deficiencies due to maldigestion of starch and the high acidity of abomasal fluid.

Intensified specimen collection to improve tuberculosis diagnosis in children from Rural South Africa, an observational study

BACKGROUND

In drug-resistant TB settings, specimen collection is critical for drug-susceptibility testing (DST). This observational study included multiple specimen types collected from pediatric TB suspects with the aim to determine diagnostic yield and inform clinical practice in children with drug-resistant and drug-susceptible TB.

METHODS

From 03/2009-07/2010, TB suspects aged ≥6 months and ≤12 years were recruited among outpatient and inpatient settings. Subjects were new TB suspects or had persistent symptoms despite ≥2 months of TB treatment. The protocol included collection of a single blood and urine specimen, a single sputum induction and, if inpatients and <5 years of age, collection of 3 gastric aspirates (GA). Samples were cultured on solid and/or liquid media. DST was by 1% proportion method.

RESULTS

Among 118 children with possible, probable or confirmed TB, the mean age was 4.9 years [SD 3.2] and 64 (62%) of those tested were HIV-positive. Eight (7%) subjects were culture-positive from at least one specimen; yield did not differ by HIV status or TB treatment history. Among those with positive cultures, 7/8 (88%) were from induced sputum, 5/6 (83%) from GA, 3/8 (38%) from blood, and 3/7 (43%) from urine. In subjects with both induced sputum and GA collection, sputum provided one additional case compared to GA. Multidrug resistant (MDR)-TB was detected by urine culture alone in one child >5 years old. Pan-resistant extensively drug resistant (XDR)-TB was identified by cultures from all sites in one subject.

CONCLUSIONS

TB was cultured from HIV-positive and -negative children, and allowed for identification of MDR and XDR-TB cases. Urine and induced sputum each provided an additional TB diagnosis and, when compared to GA, may be considered a less invasive, same-day method of specimen collection for childhood TB suspects. This study illustrates the continued challenges and limitations of available strategies for pediatric TB diagnostics.

[Transmission route of H. pylori]

The incidence of Helicobacter pylori (H. pylori) infection is rapidly decreased in Japan. H. pylori infection is mainly acquired in the first 2 years life and the risk of infection declines rapidly after 5 years of age. Person-to-person transmission in the family appears to be the predominant and in the population with low prevalence, several studies showed the infected mother is likely to be the main source of the infection. H. pylori can be detected from vomitus, saliva and cathartic stools and the possibility of source of infection. Waterborne infection is unlikely in the developed countries.

[Harnessing nature for treating infectious and autoimmune diseases: good and bad bacteria]

Clostridium difficile is the etiologic agent of nosocomial and community-acquired diarrhea associated with exposure to antibiotics that disrupt the normal colonic flora. As antibacterials currently used for primary C. difficile infections favor recurrences, new methods able to neutralize the bacterium without affecting the gut microbiota are badly needed. Complementary treatment with probiotic agents to reconstitute the physiologicaL intestinal flora does not yield any consistent benefit. In recent years, fecal transplantation has been used in the English-speaking countries with cure rates of about 87%. Fecal microbiota transplantation (FMT) holds considerable promise as a therapy for recurrent Clostridium difficile infection, but well-designed, randomized-controlled trials and Long-term follow-up registries are stilt required. These are needed to identify the right patient, efficacy and safety profile of FMT before this approach can be widely advocated. Another aspect of bad/good parasites are the use of helminth or helminth ova for treating autoimmune diseases, especially those affecting the gut.

Soybean oligosaccharides alter colon short-chain fatty acid production and microbial population in vitro

This study was conducted to the determine fermentation characteristics of soybean oligosaccharides (SBOS) in an in vitro system. Digesta collected from the colon of Huanjiang mini-pigs was used as inoculums, and SBOS (0.2 g per 10 mL fermentation broth) was used as substrate during the in vitro fermentation. The inoculum or inoculum + glucose (0.2 g) was used as negative or positive control, respectively. The slurry was fermented in an anaerobic chamber and gas production (GP) recording was taken after 48 h of incubation by referring to the moving scale on the plunger of the glass syringes, and then GP parameters, pH value, NH(3)-N content, short chain fatty acid (SCFA) levels, and microbial community in the fermentation broth were determined. For gas production parameters, pH, and fermentation product determination after 1, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 28, 32, 36, 42, and 48 h of incubation, SBOS and glucose demonstrated similar responses compared to control including increase maximal gas production, decreased lag time, decreased pH, and accumulation of NH(3) and increased SCFA. The exception was rate of GP, which was higher (P < 0.05) for SBOS compared with glucose. Incubation with SBOS increased (P < 0.05) the microbial diversity and population of Bifidobacterium and Lactobacillus but decreased (P < 0.05) Escherichia and Streptococcus when compared with incubation with glucose. These findings suggested that the SBOS can improve the gut microbiota balance in colon and modulate its metabolism.

Effect of high-dose nano-selenium and selenium-yeast on feed digestibility, rumen fermentation, and purine derivatives in sheep

The aim of this study was to evaluate the effect of nano-selenium (NS) and yeast-selenium (YS) supplementation on feed digestibility, rumen fermentation, and urinary purine derivatives in sheep. Six male ruminally cannulated sheep, average 43.32 ± 4.8 kg of BW, were used in a replicated 3 × 3 Latin square experiment. The treatments were control (without NS and YS), NS with 4 g nano-Se (provide 4 mg Se), and YS with 4 g Se-yeast (provide 4 mg Se) per kilogram of diet dry matter (DM), respectively. Experimental periods were 25 days with 15 days of adaptation and 10 days of sampling. Ruminal pH, ammonia N concentration, molar proportion of propionate, and ratio of acetate to propionate were decreased (P < 0.01), and total ruminal VFA concentration was increased with NS and YS supplementation (P < 0.01). In situ ruminal neutral detergent fiber (aNDF) degradation of Leymus chinensis (P < 0.01) and crude protein (CP) of soybean meal (P < 0.01) were significantly improved by Se supplementation. Digestibilities of DM, organic matter, crude protein, ether extract, aNDF, and ADF in the total tract and urinary excretion of purine derivatives were also affected by feeding Se supplementation diets (P < 0.01). Ruminal fermentation was improved by feeding NS, and feed conversion efficiency was also increased compared with YS (P < 0.01). We concluded that nano-Se can be used as a preferentially available selenium source in ruminant nutrition.

Feed restriction enhances the depressive effects of erythromycin on equine hindgut microbial metabolism in vitro

Equine typholocolitis is a sporadic diarrheal disease causing high mortality rates. One of the risk factors responsible for this is the oral application of the macrolide antibiotic erythromycin. The aim of the present in vitro study was to investigate whether erythromycin in combination with feed restriction provokes changes in microbial hindgut metabolism and could therefore be involved in the pathogenesis of equine typhlocolitis. As application of erythromycin and feed restriction are risk factors for equine typhlocolitis, both factors were chosen to investigate their individual and combined effects on hindgut microbial metabolism. The colon simulation technique (Cositec) was used to evaluate biochemical parameters of microbial metabolism. Production rates of the acetate, proprionate and butyrate were measured as quantitative parameters of microbial fermentation. Application of erythromycin (10 mg/d) predominantly decreased the production rates of propionate. Reducing the fermentable substrate to 30% induced an even more pronounced impairment. The detrimental effects of feed restriction on the production rates of short-chain fatty acids (SCFA) were enhanced when feed restriction was combined with the application of erythromycin. Irrespective of erytrhomycin, the butyrate fermentation rate was completely inhibited by feed restriction within two days after start of restriction. The reduction in butyrate fermentation rate has to be discussed as a pathophysiological factor for the onset of acute typhlocolitis.

The prevalence of overgrowth by aerobic bacteria in the small intestine by small bowel culture: relationship with irritable bowel syndrome

OBJECTIVES

Many studies have linked irritable bowel syndrome (IBS) with small intestinal bacterial overgrowth (SIBO), although they have done so on a qualitative basis using breath tests even though quantitative cultures are the hallmark of diagnosis. The purpose of this study was to underscore the frequency of SIBO in a large number of Greeks necessitating upper gastrointestinal (GI) tract endoscopy by using quantitative microbiological assessment of the duodenal aspirate.

METHODS

Consecutive subjects presenting for upper GI endoscopy were eligible to participate. Quantitative culture of aspirates sampled from the third part of the duodenum during upper GI tract endoscopy was conducted under aerobic conditions. IBS was defined by Rome II criteria.

RESULTS

Among 320 subjects enrolled, SIBO was diagnosed in 62 (19.4%); 42 of 62 had IBS (67.7%). SIBO was found in 37.5% of IBS sufferers. SIBO was found in 60% of IBS patients with predominant diarrhea compared with 27.3% without diarrhea (P = 0.004). Escherichia coli, Enterococcus spp and Klebsiella pneumoniae were the most common isolates within patients with SIBO. A step-wise logistic regression analysis revealed that IBS, history of type 2 diabetes mellitus and intake of proton pump inhibitors were independently and positively linked with SIBO; gastritis was protective against SIBO.

CONCLUSIONS

Using culture of the small bowel, SIBO by aerobe bacteria is independently linked with IBS. These results reinforce results of clinical trials evidencing a therapeutic role of non-absorbable antibiotics for the management of IBS symptoms.

Effects of Euphorbia esula L. (leafy spurge) on cattle and sheep in vitro fermentation and gas production

BACKGROUND

Euphorbia esula L. (leafy spurge) is indigenous to Eurasia and has been known to cause grazing aversion in ruminant species. As a result, E. esula encroachment has negatively impacted rangelands in the Northern Great Plains and Intermountain West of the USA, as well as southern Canada. Our objectives were to evaluate the effect of increasing concentrations of E. esula on in vitro dry matter digestibility (DMD) and gas production. Two ruminally-cannulated cows and ewes were used as rumen inoculum donors. To accomplish objectives, two studies were conducted. In study 1, animals were fed exclusively a barley hay (12% crude protein (CP), 55.4% neutral detergent fiber (NDF), DM basis) diet; whereas in study 2, animals were fed a diet of 15% E. esula (21.9% CP, 48% NDF, DM basis) and 85% barley hay based on previous day intake.

RESULTS

The 24 and 48 h in vitro and 96 h gas production indicate that, regardless of inoculum source or substrate fermented, DMD was not influenced. Differences, however, were consistently observed across studies for NDF disappearance.

CONCLUSION

Regardless of inoculum source NDF disappearance was greater when substrate being fermented contained 0%, 80%, or 100% E. esula.

Effects of tea saponins on rumen microbiota, rumen fermentation, methane production and growth performance--a review

Reducing methane emission from ruminant animals has implications not only for global environmental protection but also for efficient animal production. Tea saponins (TS) extracted from seeds, leaves or roots of tea plant are pentacyclic triterpenes. They have a lasting antiprotozoal effect, but little effect on the methanogen population in sheep. There was no significant correlation between the protozoa counts and methanogens. The TS decreased methanogen activity. It seems that TS influenced the activity of the methanogens indirectly via the depressed ciliate protozoal population. The TS addition decreased fungal population in the medium containing rumen liquor in in vitro fermentation, but no such effect was observed in the rumen liquor of sheep fed TS. Tea saponins had a minor effect on the pattern of rumen fermentation and hence on nutrient digestion. When added at 3 g/day in diets, TS could improve daily weight gain and feed efficiency in goats. No positive associative effect existed between TS and disodium fumarate or soybean oil on methane suppression. Inclusion of TS in diets may be an effective way for improving feed efficiency in ruminants.

Clostridiaceae and Enterobacteriaceae as active fermenters in earthworm gut content

The earthworm gut provides ideal in situ conditions for ingested heterotrophic soil bacteria capable of anaerobiosis. High amounts of mucus- and plant-derived saccharides such as glucose are abundant in the earthworm alimentary canal, and high concentrations of molecular hydrogen (H(2)) and organic acids in the alimentary canal are indicative of ongoing fermentations. Thus, the central objective of this study was to resolve potential links between fermentations and active fermenters in gut content of the anecic earthworm Lumbricus terrestris by 16S ribosomal RNA (rRNA)-based stable isotope probing, with [(13)C]glucose as a model substrate. Glucose consumption in anoxic gut content microcosms was rapid and yielded soluble organic compounds (acetate, butyrate, formate, lactate, propionate, succinate and ethanol) and gases (carbon dioxide and H(2)), products indicative of diverse fermentations in the alimentary canal. Clostridiaceae and Enterobacteriaceae were users of glucose-derived carbon. On the basis of the detection of 16S rRNA, active phyla in gut contents included Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, Tenericutes and Verrucomicrobia, taxa common to soils. On the basis of a 16S rRNA gene similarity cutoff of 87.5%, 82 families were detected, 17 of which were novel family-level groups. These findings (a) show the large diversity of soil taxa that might be active during gut passage, (b) show that Clostridiaceae and Enterobacteriaceae (fermentative subsets of these taxa) are selectively stimulated by glucose and might therefore be capable of consuming mucus- and plant-derived saccharides during gut passage and (c) indicate that ingested obligate anaerobes and facultative aerobes from soil can concomitantly metabolize the same source of carbon.

Analysis of Nsukka metropolitan abattoir solid waste and its bacterial contents in south eastern Nigeria: public health implication

This study was conducted to determine the quantum of waste generation and management and presence of major bacteria genera of public health importance in Nsukka municipal abattoir/slaughter house. The environment and public health implications of unhygienic sanitary condition at the abattoir and environs as a consequence of poor waste disposal and management were studied. A total of 194 kg of solid (rumen/stomach) wastes was generated daily without any clearly defined system of disposal and management. Forty-five rumen/stomach waste samples were examined for bacterial isolates using standard procedures. The isolation frequency showed that E. coli, Bacillus sp., and Staphylococcus sp. were more frequently isolated, followed by Streptococcus sp., Salmonella sp., and Campylobacter sp. Appropriate strategies for efficient solid waste disposal and management in our abattoirs were recommended.

Detection and analysis of the bacterium, Xylella fastidiosa, in glassy-winged sharpshooter, Homalodisca vitripennis, populations in Texas

The glassy-winged sharpshooter, Homalodisca vitripeninis Germar (Hemiptera: Cicadellidae), is a xylophagous insect that is an endemic pest of several economically important plants in Texas. H. vitripennis is the main vector of Xylella fastidiosa Wells (Xanthomonadales: Xanthomonadaceae), the bacterium that causes Pierce's disease of grapevine and can travel long distances putting much of Texas grape production at risk. Understanding the movement of H. vitripennis populations capable of transmitting X. fastidiosa into Pierce's-disease-free areas is critical for developing a management program for Pierce's disease. To that end, the USDA-APHIS has developed a program to sample vineyards across Texas to monitor populations of H. vitripennis. From this sampling, H vitripennis collected during 2005 and 2006 over the months of May, June, and July from eight vineyards in different regions of Texas were recovered from yellow sticky traps and tested for the presence of X. fastidiosa. The foregut contents were vacuum extracted and analyzed using RT-PCR to determine the percentage of H. vitripennis within each population that harbor X. fastidiosa and have the potential to transmit this pathogen. H. vitripennis from vineyards known to have Pierce's disease routinely tested positive for the presence of X. fastidiosa. While almost all H. vitripennis collected from vineyards with no history of Pierce's disease tested negative for the presence of the pathogen, three individual insects tested positive. Furthermore, all three insects were determined, by DNA sequencing, to be carrying a strain of X. fastidiosa homologous to known Pierce's disease strains, signifying them as a risk factor for new X. fastidiosa infections.

[The role of biliary decompression and correction of dysbiosis in the treatment of obstructive jaundice]

The article providing in-depth analysis of pathogenesis of obstructive jaundice shows that this disease is manifest not only as changes at the hepatic level (cholestasis, cholehemia, cholangitis, cholangio- and lymphovenous shunts, hepatic encephalopathy) but also as marked dysbiotic disturbances due to anacholia and toxic metabolites that cause bacterial translocation and endotoxemia complicating liver insufficiency. Based on the literary data and original observations, a new scheme for the treatment of obstructive jaundice is proposed including simultaneous correction of both components of hepatoenteric turnover, also, it permits to improve the outcome of the postoperative period.

Fine-needle aspiration biopsy: a first-line diagnostic procedure in paediatric tuberculosis suspects with peripheral lymphadenopathy?

OBJECTIVE

To evaluate the diagnostic yield and time to diagnosis of fine-needle aspiration biopsy (FNAB) vs. routine respiratory specimens collected from children with a palpable peripheral lymph node mass and symptoms suspicious of tuberculosis (TB).

DESIGN

We performed a retrospective review of laboratory records at Tygerberg Hospital over a 4-year period from January 2003 to December 2006. All children (aged <13 years) in whom an FNAB and other mycobacterial specimens were collected as part of their diagnostic workup were included.

RESULTS

In 95 children, the following specimens were collected: FNAB (n = 95), gastric aspirates (n = 142), other respiratory specimens (n = 36), non-respiratory specimens (n = 26). Mycobacterial disease was diagnosed in 70 (73.7%) patients. Children without respiratory specimens (n = 6) and/or with Mycobacterium bovis bacille Calmette-Guérin disease (n = 15) were excluded from comparative analysis. In the remainder, FNAB was positive in 45/74 (60.8%) vs. any respiratory specimen in 29/74 (39.2%, P < 0.001). The mean time to bacteriological diagnosis with FNAB was 7.1 days (95%CI 4.2-10.1) compared to 22.5 days (95%CI 15.8-29.1) for any respiratory specimen.

CONCLUSION

FNAB is a simple, rapid and effective modality for achieving confirmation of mycobacterial disease in paediatric TB suspects with a palpable peripheral lymph node mass.

Influence of different periods of exposure to hot environment on rumen function and diet digestibility in sheep

Effects of different periods of exposure to hot environments on rumen function, diet digestibility and digesta passage rate were studied in four adult not-pregnant Sardinian ewes housed in a climatic chamber. The ewes were kept in individual metabolic cages. The trial lasted 83 days; 17 days were spent under thermal comfort conditions (TC) [temperature-humidity index (THI) = 65.0 +/- 2.0], followed by 49 days under elevated THI (ETHI: THI = 82.0 +/- 2.5) and 17 days under thermal comfort (TC; THI = 65.0 +/- 1.0). Five digestibility and passage rate trials were carried out during the 83 days. Trials 1 and 5 were carried out under TC; trials 2, 3 and 4 were carried out under ETHI. Values of rectal temperatures (39.7 +/- 0.3 degrees C) and respiratory rate (118.4 +/- 31.8 breaths/min) indicated that sheep under ETHI were heat-stressed. Heat stress caused an increase (P < 0.01) in water intake, and reductions (P < 0.05) in dry matter intake, rumen pH, rumen cellulolytic and amylolytic bacteria count, rumen osmolarity, organic matter, dry matter, neutral detergent fibre, acid detergent fibre and non-structural carbohydrates digestibility coefficients, and a reduction of digesta passage rates. Under ETHI, diet digestibility and passage rate of digesta were reduced in a time-dependent fashion. Variation of diet digestibility under ETHI was not related to passage rate of digesta and feed intake. Reduction of cellulolytic and amylolytic bacteria and the adaptive response to hot environment seem to be related to alteration of digestibility observed in ewes chronically exposed to hot environment.

Coastal fish farms are settlement sites for juvenile fish

Two south-west Mediterranean fish farms were monitored over a period of 22 months to test if sea-cage fish farms act as settlement habitats for juvenile fish. Twenty juvenile fish species were found to settle at farms throughout the year. Fish assemblage composition varied markedly over time and was dependent on the spawning period for each species. The most abundant species were Obladamelanura, Atherina sp., Diplodussargus, Boopsboops and Lizaaurata. Up to 3783+/-1730 individuals/cage were found closely associated with the cages. Highest densities were observed during the warmer summer and autumn months. Zooplankton sampling and stomach content analyses of the most abundant species were done to assess prey availability, selectivity and diet overlap among species. Copepods were the main prey item for all juvenile fish species, irrespective of fish size. Ivlev's Index indicated that food was not a limiting factor for juvenile fish at farms. Furthermore, food pellets from the farm affected the food chain by modifying the fatty acid profiles of farm-associated zooplankton and juveniles of L. aurata and O. melanura. These results show that aquaculture can directly influence the body composition of juvenile fish that recruit to sea-cage fish farms.

Prophylactic supplementation of caprylic acid in feed reduces Salmonella enteritidis colonization in commercial broiler chicks

Salmonella Enteritidis is a major foodborne pathogen for which chickens serve as reservoir hosts. Reducing Salmonella Enteritidis carriage in chickens would reduce contamination of poultry meat and eggs with this pathogen. We investigated the prophylactic efficacy of feed supplemented with caprylic acid (CA), a natural, generally recognized as safe eight-carbon fatty acid, for reducing Salmonella Enteritidis colonization in chicks. One hundred commercial day-old chicks were randomly divided into five groups of 20 birds each: CA control (no Salmonella Enteritidis, CA), positive control (Salmonella Enteritidis, no CA), negative control (no Salmonella Enteritidis, no CA), and 0.7 or 1% CA. Water and feed were provided ad libitum. On day 8, birds were inoculated with 5.0 log CFU of Salmonella Enteritidis by crop gavage. Six birds from each group were euthanized on days 1, 7, and 10 after challenge, and Salmonella Enteritidis populations in the cecum, small intestine, cloaca, crop, liver, and spleen were enumerated. The study was replicated three times. CA supplementation at 0.7 and 1% consistently decreased Salmonella Enteritidis populations recovered from the treated birds. Salmonella Enteritidis counts in the tissue samples of CA-treated chicks were significantly lower (P < 0.05) than those of control birds on days 7 and 10 after challenge. Feed intake and body weight did not differ between the groups. Histological examination revealed no pathological changes in the cecum and liver of CA-supplemented birds. The results suggest that prophylactic CA supplementation through feed can reduce Salmonella Enteritidis colonization in day-old chicks and may be a useful treatment for reducing Salmonella Enteritidis carriage in chickens.

Ecophysiology of the developing total bacterial and lactobacillus communities in the terminal small intestine of weaning piglets

Weaning of the pig is generally regarded as a stressful event which could lead to clinical implications because of the changes in the intestinal ecosystem. The functional properties of microbiota inhabiting the pig's small intestine (SI), including lactobacilli which are assumed to exert health-promoting properties, are yet poorly described. Thus, we determined the ecophysiology of bacterial groups and within genus Lactobacillus in the SI of weaning piglets and the impact of dietary changes. The SI contents of 20 piglets, 4 killed at weaning (only sow milk and no creep feed) and 4 killed at 1, 2, 5, and 11 days post weaning (pw; cereal-based diet) were examined for bacterial cell count and bacterial metabolites by fluorescence in situ hybridization (FISH). Lactobacilli were the predominant group in the SI except at 1 day pw because of a marked reduction in their number. On day 11 pw, bifidobacteria and E. coli were not detected, and Enterobacteriaceae and members of the Clostridium coccoides/Eubacterium rectale cluster were only found occasionally. L. sobrius/L. amylovorus became dominant species whereas the abundance of L. salivarius and L. gasseri/johnsonii declined. Concentration of lactic acid increased pw whereas pH, volatile fatty acids, and ammonia decreased. Carbohydrate utilization of 76 Lactobacillus spp. isolates was studied revealing a shift from lactose and galactose to starch, cellobiose, and xylose, suggesting that the bacteria colonizing the SI of piglets adapt to the newly introduced nutrients during the early weaning period. Identification of isolates based on partial 16S rRNA gene sequence data and comparison with fermentation data furthermore suggested adaptation processes below the species level. The results of our study will help to understand intestinal bacterial ecophysiology and to develop nutritional regimes to prevent or counteract complications during the weaning transition.

A comparison of sampling sites, digesta and microbial markers, and microbial references for assessing the postruminal supply of nutrients in dairy cows

This study evaluated the impact of some methodological factors on the flows of nutrients at the omasal canal and duodenum of dairy cows fed corn-based diets. Three ruminally and duodenally cannulated cows were assigned to an incomplete 4 x 4 Latin square with four 14-d periods and fed diets formulated to contain different amounts and ruminal degradabilities of crude protein. Samples from the omasal canal and duodenum were obtained and processed according to methodologies routinely used in our laboratories and elsewhere. Methodological factors that were evaluated included microbial references and markers, digesta markers, and sampling sites (techniques). Considerable variation was found for the compositions of microbial references and their impact on the intestinal supply of microbial nonammonia nitrogen. Likewise, it appears that variation in measuring the ruminal outflow of nitrogen fractions of microbial and dietary origin could be reduced by using 15N rather than purines as microbial markers. Sampling from the omasum and duodenum resulted in differences for ruminal outflow and site of digestion as well as digestibility of some nutrients, particularly nitrogen fractions and starch. A sizable portion of this variation was associated with deviations from the assumed ideal behavior of digesta markers and collection of samples that were unrepresentative of true digesta. Collectively, outcomes from this study indicate that more research will be required to determine the accuracy of nutrient flows and the agreement between measurements at the omasal canal and duodenum when dairy cows are fed a variety of diets under different feeding systems. Therefore, caution is recommended when extrapolating or interpreting the underlying biology of published results as well as the results of their application (e.g., model parameters and predictions).

New phospholipase A1-producing bacteria from a marine fish

Phospholipase A1 is a hydrolytic enzyme that catalyzes the removal of the acyl group from position 1 of glycerophospholipids to form 2-acyl lysophospholipids. Lysophospholipids are used in foods, cosmetics, and pharmaceuticals as surfactants. Novel forms of phospholipase A1 that function at low temperatures are desirable for use in lipophilic systems in food processing. However, there is currently little variety in the available sources of phospholipase A1. Given this situation, we screened the intestinal contents of marine animals for phospholipase A1-producing bacteria. Colonies that formed a halo on K28CP screening medium and that grew in K28 medium were cultured in liquid K28 medium, and the supernatant was retrieved for analysis. Phosphatidylcholine was added to the culture supernatant, and the product of the reaction was analyzed by using TLC. For culture supernatants that were able to generate lysophosphatidylcholine, synthetic phosphatidylcholines were added, and the site of the reaction was determined by analyzing the fatty acid compositions of the lysophosphatidylcholines generated by GLC. A bacterial isolate from a flatfish, which we named HFKI0020, was found to have phospholipase A1 activity at low temperatures. We determined that the isolate HFKI0020 is closely related to Pseudomonas by using 16S rDNA sequence analysis and by characterizing the isolate with respect to its physiologic and biochemical properties. From the intestinal contents of a marine fish, we successfully isolated a bacterium that secretes phospholipase A1 that is active at low temperatures.

[Morphofunctional development of the rabbits cecum in ontogenesis]

Quick growing capacities of the caecum, bacterial number in its contents, and enzymal activities of caecal microbes were shown in the rabbit of a 20-day age. In addition, 45-day old rabbits reveal that the factors of caecal digestions reach their maximum, and then drop again at 60-day age, when the mass of the caecum in calculation on unit of the alive mass approaches to value typical of adult animal. Final shaping of the caecum functional capacities occurs at three-month age.

The response of gastrointestinal microbiota to avilamycin, butyrate, and plant extracts in early-weaned pigs

An experiment was designed to evaluate the effects of 3 different additives on the gastrointestinal microbiota of early-weaned pigs. Early-weaned (18 to 22 d; n = 32) pigs (6.0 +/- 0.10 kg of BW) from 8 litters were randomly distributed into 8 pens. Each pen was assigned 1 of 4 dietary treatments: a prestarter or control diet, the control diet with 0.04% avilamycin (AB), with 0.3% sodium butyrate, or with 0.03% plant extract mixture (XT; standardized mixture with 5% (wt/wt) carvacrol extracted from Origanum spp., 3% cinnamaldehyde extracted from Cinnamonum spp., and 2% capsicum oleoresin from Capsicum annum). At the end of the experimental period, 8 pigs per treatment were killed, and samples of their intestinal content were taken. The total bacterial load along the gastrointestinal tract (GIT; stomach, jejunum, cecum, and distal colon) and the lactobacilli and enterobacteria in the jejunum and cecum were measured by quantitative PCR. The total microbial counts along the GIT did not differ among the diets, but there was an increase in the lactobacilli:enterobacteria ratio in the cecum of the piglets on the XT diet (P = 0.003). Restriction fragment length polymorphism of the PCR-amplified V3, V4, and V5 regions of the 16S rDNA gene showed changes in the structure of the microbial community in the jejunum. Dendrograms grouped animals by diets; control with 0.3% sodium butyrate was the treatment that promoted the biggest changes in the microbial ecosystem, followed by AB and then XT. Biodiversity increased when using additives compared with the control diet (P = 0.002). Microbial metabolic activity along the hindgut was studied using the concentration of purine bases and carbohydrase activities. Different patterns for purine bases were observed between diets (diet x intestinal section, P = 0.01). The control diet reached a maximum purine base concentration at the end of the colon, whereas that of the AB diet was reached at the cecum. We could not detect any cellulase or xylanase activities in animals of this age. Appreciable amylase and amylopectinase activities were found, but they did not differ between diets. The results suggest that the effects of avilamycin, butyrate, or the plant extract would not be related to a reduction in the number of total bacteria inhabiting different sections of the GIT but rather to changes in the ecological structure and metabolic activity of the microbial community.

Microbial diversity of intestinal contents and mucus in rainbow trout (Oncorhynchus mykiss)

AIMS

The aim of this study was to understand the microbial community of intestinal contents and mucosal layer in the intestine of rainbow trout by means of culture-dependent conventional and independent molecular techniques.

METHODS AND RESULTS

Forty-one culturable microbial phylotypes, and 39 sequences from 16S rRNA and two from 18S rRNA genes, were retrieved. Aeromonadaceae, Enterobacteriaceae and Pseudomonadaceae representatives were the dominant cultured bacteria. Genomic DNA isolated from intestinal contents and mucus was used to generate 104 random clones, which were grouped into 32 phylotypes at 99% minimum similarity, most of which were affiliated with Proteobacteria (>70% of the total). However, unlike library C (intestinal contents), the phyla Bacteroidetes and Fusobacteria were not found in intestinal mucus (library M), indicating that the microbiota in the gut mucus was different from that of the intestinal contents. Twelve sequences were retrieved from denaturing gradient gel electrophoresis analysis, and dominant bands were mostly related to Clostridium.

CONCLUSIONS

Many novel sequences that have not been previously recognized as part of the intestinal flora of rainbow trout were retrieved.

SIGNIFICANCE AND IMPACT OF THE STUDY

The fish gut harbours a larger bacterial diversity than previously recognized, and the diversity of gut mucus is different from that of intestinal contents.

Increased amount of Bifidobacterium thermacidophilum and Megasphaera elsdenii in the colonic microbiota of pigs fed a swine dysentery preventive diet containing chicory roots and sweet lupine

AIMS

To investigate which specific bacterial species that were stimulated or inhibited in the proximal colon of pigs when a fructan-rich diet was compared with a diet that contained resistant carbohydrates. The study focussed especially on Bifidobacterial species by using a noncultureable approach.

METHODS AND RESULTS

Terminal restriction fragment length polymorphism (T-RFLP) was used to describe differences in the total colonic microbiota as well as in the populations of Bifidobacterium spp. in pigs fed with a fructan-rich diet and a diet containing resistant carbohydrates. The fructan-rich diet has previously been shown to prevent swine dysentery caused by Brachyspira hyodysenteriae. The T-RFLP profiling, 16S rRNA gene cloning and in situ hybridization showed that the pigs fed with the fructan-rich diet had a higher proportion of Bifidobacterium thermacidophilum subsp. porcinum and Megasphaera elsdenii.

CONCLUSIONS

These findings suggested that the bacterial fructan fermentation occurring in the porcine colon might be cross-feeding of lactate produced by B. thermacidophilum and used by M. elsdenii.

SIGNIFICANCE AND IMPACT OF THE STUDY

B. thermacidophilum and M. elsdenii may be the course of the inhibition of the pathogenic bacteria Brach. hyodysenteriae in colon of pigs when they are fed fructan-rich diets.

Quantification of ruminalClostridium proteoclasticumby real-time PCR using a molecular beacon approach

AIMS

All members of the ruminal Butyrivibrio group convert linoleic acid (cis-9,cis-12-18:2) via conjugated 18:2 metabolites (mainly cis-9,trans-11-18:2, conjugated linoleic acid) to vaccenic acid (trans-11-18:1), but only members of a small branch, which includes Clostridium proteoclasticum, of this heterogeneous group further reduce vaccenic acid to stearic acid (18:0, SA). The aims of this study were to develop a real-time polymerase chain reaction (PCR) assay that would detect and quantify these key SA producers and to use this method to detect diet-associated changes in their populations in ruminal digesta of lactating cows.

METHODS AND RESULTS

The use of primers targeting the 16S rRNA gene of Cl. proteoclasticum was not sufficiently specific when only binding dyes were used for detection in real-time PCR. Their sequences were too similar to some nonproducing strains. A molecular beacon probe was designed specifically to detect and quantify the 16S rRNA genes of the Cl. proteoclasticum subgroup. The probe was characterized by its melting curve and validated using five SA-producing and ten nonproducing Butyrivibrio-like strains and 13 other common ruminal bacteria. Analysis of ruminal digesta collected from dairy cows fed different proportions of starch and fibre indicated a Cl. proteoclasticum population of 2-9% of the eubacterial community. The influence of diet on numbers of these bacteria was less than variations between individual cows.

CONCLUSIONS

A molecular beacon approach in qPCR enables the detection of Cl. proteoclasticum in ruminal digesta. Their numbers are highly variable between individual animals.

SIGNIFICANCE AND IMPACT OF THE STUDY

SA producers are fundamental to the flow of polyunsaturated fatty acid and vaccenic acid from the rumen. The method described here enabled preliminary information to be obtained about the size of this population. Further application of the method to digesta samples from cows fed diets of more variable composition should enable us to understand how to control these bacteria in order to enhance the nutritional characteristics of ruminant-derived foods, including milk and beef.