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.

Microbacterium caowuchunii sp. nov. and Microbacterium lushaniae sp. nov., isolated from plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of PR China.

Four novel bacterial strains (ST-M6T, L-033, L-031T and Z-333) were isolated from the intestinal contents of plateau pikas (Ochotona curzoniae) collected on the Qinghai-Tibet Plateau, PR China. Cells were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, capsuled and short-rod-shaped. Phylogenetic analyses based on the 16S rRNA gene sequences and 387 core genes indicated that the four isolates belong in the genus Microbacterium and clearly separate from recognized species. The two type strains (ST-M6T and L-031T) shared low 16S rRNA similarity, average nucleotide identity values and digital DNA-DNA hybridization relatedness with their phylogenetic neighbours (Microbacterium ginsengisoli DSM 18659T, Microbacterium hatanonis DSM 19179T, Microbacterium rhizomatis JCM 30598T, Microbacterium radiodurans CCTCC M208212T, Microbacterium oleivorans DSM 16091T and Microbacterium arborescens DSM 20754T). The genomic DNA G+C contents of strains ST-M6T and L-031T were 70.4 and 70.7 mol%, respectively. The major cellular fatty acids of strain ST-M6T were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, in contrast to anteiso-C17 : 0, anteiso-C15 : 0 and anteiso-C17 : 1 ω9c of strain L-031T. Both type strains (ST-M6T and L-031T) were glycolate test positive and shared the following common features: MK-11 and MK-12 as major menaquinones; rhamnose, ribose, mannose and galactose as major cell-wall sugars; diphosphatidylglycerol, phosphatidylglycerol and two glycolipids as polar lipids; and ornithine, alanine, glycine and glutamic acid as cell-wall amino acids. Comparing the phenotypic, phylogenetic and chemotaxonomic features of the four strains and their related taxa, strains ST-M6T and L-031T represent two novel species of the genus Microbacterium, for which the names Microbacterium caowuchunii sp. nov. (type strain ST-M6T=CGMCC 1.16364T=DSM 104058T) and Microbacterium lushaniae sp. nov. (type strain L-031T =CGMCC 1.16363T=DSM 106170T) are proposed.

Diagnosis of Tuberculosis Using Gastric Aspirates in Pediatric Patients in Haiti.

BACKGROUND: We aimed to determine whether the Xpert MTB/RIF (Xpert) assay is a useful adjunct to culture for the rapid diagnosis of tuberculosis (TB) using gastric lavage aspirates (GLAs) in children aged < 5 years. METHODS: We reviewed the yield from diagnostic modalities in children suspected of having TB followed at an infectious disease research and treatment center in Port-au-Prince, Haiti, from 2011 to 2016. RESULTS: In 187 children clinically diagnosed with TB, a microbiologic diagnosis could be established in 40 (21%). Cultures, Xpert, and smears were positive in 30 (19%), 28 (17%), and 3 (1.6%) children, respectively. Ten cases that would not have been diagnosed by culture alone were found by the use of the Xpert assay. Collecting 2 GLA samples optimized microbiologic yield. CONCLUSIONS: In GLAs, Xpert increased the yield of microbiologically documented cases by 33%. Additionally, the rapidity of diagnosis potentially makes Xpert a valuable adjunct in initiating treatment for TB in children. Smear microscopy has low sensitivity in GLA and did not add to the documented cases. Our findings also highlight the low rate of microbiologic confirmation of clinically diagnosed TB.

Pathological changes, distribution and detection of Brucella melitensis in foetuses of experimentally-infected does.

BACKGROUND: Brucellosis of goats is caused by Brucella melitensis. It is a re-emerging zoonotic disease in many countries due to transmission from domestic animals and wildlife such as ibex, deer and wild buffaloes. OBJECTIVE: To describe the pathological changes, identification and distribution of B. melitensis in foetuses of experimentally infected does. METHODS: Twelve female goats of approximately 90 days pregnant were divided into 4 groups. Group 1 was exposed intra-conjunctival to 100 µL of sterile PBS while goats of Groups 2, 3 and 4 were similarly exposed to 100 µL of an inoculum containing 109 CFU/mL of live B. melitensis. Goats of these groups were killed at 15, 30 and 60 days post-inoculation, respectively. Foetal fluid and tissues were collected for bacterial identification (using direct bacterial culture, PCR and immuno-peroxidase staining) and histopathological examination. RESULTS: Bilateral intra-conjunctival exposure of pregnant does resulted in in-utero infection of the foetuses. All full-term foetuses of group 4 were either aborted or stillborn, showing petechiations of the skin or absence of hair coat with subcutaneous oedema. The internal organs showed most severe lesions. Immune-peroxidase staining revealed antigen distribution in all organs that became most extensive in group 4. Brucella melitensis was successfully isolated from the stomach content, foetal fluid and various other organs. CONCLUSION: Vertical transmission of caprine brucellosis was evident causing mild to moderate lesions in different organs. The samples of choice for isolation and identification of B. melitensis are stomach content as well as liver and spleen tissue.

Spatial and temporal organization of jejunal microbiota in goats during animal development process.

AIMS: This research aimed to investigate the temporal bacterial colonization relating to non-rumination, transition and rumination phases, together with the spatial organization of microbial community in the jejunal mucosa and digesta of goats. METHODS AND RESULTS: This study explored the colonization programme of the jejunal microbiota by employing 16S rRNA amplicon sequencing. The colonization pattern of jejunal bacterial community exhibited an age- and gut region-dependent progression during animal development process. Approximately 268 bacterial signatures contributed to the discrimination between gut regions, with Lactobacillus, Ruminococcus, Eubacterium and Clostridium_sensu_stricto were enriched in the jejunal digesta, and Bacteroides and unclassified bacteria were enriched in the jejunal mucosa. Intriguingly, a shift from Lactobacillus to Butyrivibrio, Eubacterium and Ruminococcus after d 20 was observed for jejunal digesta. In mucosa, Bifidobacterium, Corynebacterium, Faecalibacterium and Roseburia increased with age (P < 0·05) while Arcobacter, Bacteroides and Porphyromonas peaked at d 10. CONCLUSIONS: The jejunal bacterial community was settled after solid starter provision, which may mark the potential boundary of a timeframe for intervention in goats. The spatial heterogeneity highlighted the complicacy of ecological niches during manipulation of gut microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY: The present study extended the understanding of microbial programming and niche specific in the jejunum among different life stages and the basal cognition of persistent enhancement of nutrient utilization and decline of enteric diseases in ruminants.

Polylactose Exhibits Prebiotic Activity and Reduces Adiposity and Nonalcoholic Fatty Liver Disease in Rats Fed a High-Fat Diet.

BACKGROUND: Prebiotic dietary fibers change the intestinal microbiome favorably and provide a health benefit to the host. OBJECTIVES: Polylactose is a novel fiber, synthesized by extrusion of lactose. We evaluated its prebiotic activity by determining its fermentability, effect on the microbiota, and effects on adiposity and liver lipids in a diet-induced obesity animal model. METHODS: Male Wistar rats (4-5 wk old) were fed normal-fat (NF, 25% fat energy) or high-fat (HF, 51% fat energy) diets containing different fibers (6% fiber of interest and 3% cellulose, by weight), including cellulose (NFC and HFC, negative and positive controls, respectively), polylactose (HFPL), lactose matched to residual lactose in the HFPL diet, and 2 established prebiotic fibers: polydextrose (HFPD) and fructooligosaccharide (HFFOS). After 10 wk of feeding, organs were harvested and cecal contents collected. RESULTS: HFPL animals had greater cecum weight (3 times greater than HFC) and lower cecal pH (∼1 pH unit lower than HFC) than all other groups, suggesting that polylactose is more fermentable than other prebiotic fibers (HFPD, HFFOS; P < 0.05). HFPL animals also had increased taxonomic abundance of the probiotic species Bifidobacterium in the cecum relative to all other groups (P < 0.05). Epididymal fat pad weight was significantly decreased in the HFPL group (29% decrease compared with HFC) compared with all other HF groups (P < 0.05) and did not differ from the NFC group. Liver lipids and cholesterol were reduced in HFPL animals when compared with HFC animals (P < 0.05). CONCLUSIONS: Polylactose is a fermentable fiber that elicits a beneficial change in the gut microbiota as well as reducing adiposity in rats fed HF diets. These effects of polylactose were greater than those of 2 established prebiotics, fructooligosaccharide and polydextrose, suggesting that polylactose is a potent prebiotic.

Comparison of pH and bacterial communities in the rumen and reticulum during fattening of Japanese Black beef cattle.

We used castrated and fistulated Japanese Black beef cattle (n = 9) to measure the pH and bacterial communities in the rumen liquid, rumen solid, and reticulum liquid during early, middle, and late fattening stages (10-14, 15-22, and 23-30 months of age, respectively). The pH was measured in the rumen and reticulum during the last 13 days of each fattening stage and was significantly lower in the rumen at the early and middle fattening stage and in the reticulum during the late stage. Sequencing analysis indicated similar bacterial compositions in the rumen and reticulum liquid fractions and stability of bacterial diversity in the rumen and reticulum liquid fractions and rumen solid fraction. By contrast, major operational taxonomic units (OTUs), such as Ruminococcus bromii strain ATCC 27255 (OTU1, OTU10, and OTU15), were differently correlated to the fermentation parameters among the rumen and reticulum liquid fractions. Therefore, the long-term feeding of Japanese Black beef cattle with a high-concentrate diet might reverse the trend of pH in the rumen and reticulum during the late fattening stage, and the bacterial communities adapted to changes in fermentation by preserving their diversity throughout fattening.

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.

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.

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.

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.

Aislamiento de cepas de Enterococcus hirae productoras de enterocinas a partir del contenido intestinal de mejillón patagónico (Mytilus edulis platensis) Aislamiento de Enterococcus hirae de mejillón patagónico / Isolation of enterocin-producing Enterococcus hirae strains from the intestinal content of the Patagonian mussel (Mytilus edulis platensis)

Resumen Se aislaron del contenido intestinal del mejillón patagónico dos cepas de bacterias ácido lácticas y se caracterizaron por pruebas fenotípicas y moleculares. Los aislamientos se identificaron como Enterococcus hirae y fueron denominados E. hirae 463Me y 471Me. Por técnicas de PCR se identificó el gen de la enterocina P en ambas cepas, mientras que solamente en la cepa 471Me se detectó la enterocina hiracin JM79. Ambas cepas resultaron sensibles a los antibióticos clínicamente importantes y entre los rasgos de virulencia investigados mediante amplificación por PCR solo se pudieron detectar los genes cylL l y cylL s , sin embargo, no se observó actividad hemolítica en la prueba de agar sangre. Los sobrenadantes libres de células resultaron activos contra todas las cepas de Listeria y Enterococcus ensayadas, contra Lactobacillus plantarum TwLb 5 y contra Vibrio anguilarum V10. En óptimas condiciones de crecimiento, ambas cepas mostraron actividad inhibitoria contra Listeria innocua ATCC 33090 después de 2h de incubación. E. hirae 471Me alcanzó una actividad inhibitoria máxima de 163.840UA/ml después de 6h de incubación, mientras que el mismo valor se registró para E. hirae 463Me después de 8h. En ambos casos, la actividad antagonista alcanzó su máximo antes de lograr la fase estacionaria y permaneció estable hasta las 24h de incubación. En nuestro conocimiento, este es el primer informe de aislamiento de cepas bacteriocinogénicas de E. hirae de mejillón patagónico. La alta actividad inhibitoria y la ausencia de rasgos de virulencia indican que estos microorganismos podrían aplicarse en áreas biotecnológicas como la biopreservación de alimentos o las formulaciones probióticas.

Abstract Two bacteriocin-producing lactic acid bacterial strains were isolated from the intestinal content of the Patagonian mussel and characterized by phenotypic and molecular tests. The isolates were identified as Enterococcus hirae and named E. hirae 463Me and 471Me. The presence of the enterocin P gene was identified in both strains by PCR techniques, while enterocin hiracin JM79 was detected only in the 471Me strain. Both strains were sensitive to clinically important antibiotics and among the virulence traits investigated by PCR amplification, only cylL l and cylL s could be detected; however, no hemolytic activity was observed in the blood agar test. Cell free supernatants were active against all Listeria and Enterococcus strains tested, Lactobacillus plantarum TwLb 5 and Vibrio anguilarum V10. Under optimal growth conditions, both strains displayed inhibitory activity against Listeria innocua ATCC 33090 after 2h of incubation. E. hirae 471Me achieved a maximum activity of 163840AU/ml after 6h of incubation, while the same value was recorded for E. hirae 463Me after 8h. In both cases, the antagonist activity reached its maximum before the growth achieved the stationary phase and remained stable up to 24h of incubation. To our knowledge, this is first report of the isolation of bacteriocinogenic E. hirae strains from the Patagonian mussel. The high inhibitory activity and the absence of virulence traits indicate that they could be applied in different biotechnological areas such as food biopreservation or probiotic formulations.

Early-life lactoferrin intervention modulates the colonic microbiota, colonic microbial metabolites and intestinal function in suckling piglets.

This study reports the effects of early-life lactoferrin (LF) intervention on the colonic microbiota, intestinal function and mucosal immunity in suckling piglets. A total of 60 Duroc × Landrace × Yorkshire suckling piglets from six sows were assigned to the control (CON) and LF groups in litters. The LF group piglets were fed 0.5 g/kg body weight of LF solution per day, and the CON group piglets were fed the same dose of physiological saline for a week. Six piglets from the two groups were randomly chosen and euthanised on days 8 and 21. The LF group piglets had higher ACE and Chao1 indices of colonic microbiota than the CON group piglets (P < 0.05). In addition, the LF group piglets had a higher abundance of Roseburia (P < 0.05) and a lower abundance of Escherichia-Shigella (P < 0.05) in the colonic digesta. The LF group piglets also had a higher concentration of butyrate (P < 0.05) in the colonic digesta. Moreover, the LF group piglets had a higher gene expression of occludin (P < 0.05) in the colonic mucosa. In addition, the gene expression of MUC4 was upregulated in the LF group piglets compared with that in the CON group on day 21 (P < 0.05), and the lower gene expression of TLR-4 was found in the LF group compared with the CON group on day 8 (P < 0.05). Furthermore, the concentration of IL-10 was increased in the LF group on day 8 (P < 0.05), while the LF group piglets had a higher concentration of sIgA and lower concentrations of IL-1α and IL-1ß (P < 0.05) in the colonic mucosa. These results suggest that early-life LF intervention can modulate the composition of colonic microbiota and improve the intestinal function in suckling piglets.Key Points• Early-life LF intervention significantly modulated colon microbiota.• Early-life LF intervention can improve the colon health.• The colon microbiota plays an important role in host health.

Bacterial Characteristics in Intestinal Contents of Antibiotic-Associated Diarrhea Mice Treated with Qiweibaizhu Powder.

BACKGROUND Qiweibaizhu powder (QWBZP) is a classical prescription of traditional Chinese medicine (TCM) to treat diarrhea in pediatric patients. Its use in health care practices and interventions has shown its effect on antibiotic-associated diarrhea (AAD). It is known that the occurrence of AAD is related to an imbalance of intestinal micro-ecology. Previous studies found that QWBZP could regulate the amount of some cultured microbes and the activities of lactase and sucrase in AAD mice. In order to investigate the treatment mechanism of QWBZP on AAD, we studied the effect of QWBZP on intestinal bacteria in a community of AAD mice. MATERIAL AND METHODS AAD mice were established by administrating the mixture of gentamycin sulfate and cefradine at the dose of 23.33 mL·kg⁻¹·d⁻¹ for 5 days. Then the AAD mice were gavaged with QWBZP decoction for 4 days and gradually recovered to a normal status. On the tenth day, the intestinal contents of mice were collected, and then the DNA was extracted for 16S rRNA sequencing followed by analysis. RESULTS The analysis of bacterial 16S rRNA sequencing showed the Simpson index was decreased and the Shannon index was increased in AAD mice treated with QWBZP compared to the model group; there was no significant difference between the control group and the treatment group (P>0.05). Principle co-ordinates analysis (PCoA) indicated that there was a shorter distance between the control group and the treatment group than that between the control group and model group. At the phylum level, use of antibiotics decreased the relative abundance of Actinobacteria, Bacteroidetes, and Proteobacteria, but increased the abundance of Firmicutes and Verrucomicrobia, and the reverse changes occurred after treated with QWBZP. At the genus level, the abundance of Bacteroides and Ochrobacitrum increased in the model group, while an opposite result was observed in the treatment group. Moreover, the relative abundance of Osillospira decreased in the model group and increased in the treatment group. Genus Dorea, Coprococcus and Blautia in the model group were higher than those in the control group and further increased in the treatment group. CONCLUSIONS These results indicated that QWBZP improved the diarrhea syndrome with restoring the diversity and adjusting the structures of bacteria in mice intestine, which might reveal the therapeutic mechanism of QWBZP on treating AAD.

Diagnosis of pulmonary tuberculosis from gastric aspirate samples in nonexpectorating pediatric patients in a tertiary care hospital.

OBJECTIVES: The aim of this study was to assess the utility of Xpert assay, Ziehl-Neelsen (ZN) staining, and Mycobacteria Growth Indicator Tube (MGIT™) culture for diagnosis of pediatric pulmonary tuberculosis from gastric aspirate (GA) samples and to compare Xpert assay and ZN staining with MGIT rapid liquid culture. MATERIALS AND METHODS: GA samples from 210 nonexpectorating children, aged between 6 months to 12 years, presenting to the pediatric out-patient department (OPD) with clinical suspicion of tuberculosis (TB) were collected. The samples were tested by GeneXpert, ZN staining, and MGIT liquid culture. RESULTS: GeneXpert is a more sensitive method for rapid and early diagnosis of pediatric TB when compared with microscopy.

Microbial Ecology of Atlantic Salmon (Salmo salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota.

Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, commercial fishing through wild stock enhancements, and aquaculture production. Flowthrough (FT) hatcheries require more water than recirculating aquaculture systems (RAS), which enable up to 99% of their water to be recycled, thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of three Atlantic salmon hatcheries (RAS n = 2, FT n = 1). Gill, skin, and digesta from six juvenile fish along with tank biofilms and water were sampled from tanks in each of the hatcheries (60 fish across 10 tanks) to assess the built environment and mucosal microbiota using 16S rRNA gene sequencing. The water and tank biofilm had more microbial richness than fish mucus, while skin and digesta from RAS fish had 2 times the richness of FT fish. Body sites each had unique microbiomes (P < 0.001) and were influenced by hatchery system type (P < 0.001), with RAS being more similar. A strong association between the tank and fish microbiome was observed. Water and tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin, and digesta communities were more similar to that in the origin tank biofilm than those in all other experimental tanks, suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. Lastly, microbial diversity and mucous cell density were positively associated with fish growth and length. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome, with the skin microbiome as an important intermediate.IMPORTANCE Atlantic salmon, Salmo salar, is the most farmed marine fish worldwide, with an annual production of 2,248 million metric tons in 2016. Salmon hatcheries are increasingly changing from flowthrough toward recirculating aquaculture system (RAS) design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies of hatcheries have focused either on the fish mucosal microbiota or on the built environment microbiota but have not combined the two to understand their interactions. Our study evaluates how the water and tank biofilm microbiota influences the fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and, furthermore, how this can influence fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for beneficial phenotypes.

Georgenia wutianyii sp. nov. and Georgenia yuyongxinii sp. nov. isolated from plateau pika (Ochotona curzoniae) on the Qinghai-Tibet plateau of China.

Four novel bacterial strains, designated Z294T, Z311, Z443T and Z446, were isolated from the intestinal contents of plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of China. Cells were Gram-stain-positive, catalase-positive, oxidase-negative, aerobic, non-motile and short-rod shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four isolates belong to the genus Georgenia, but clearly separate from the currently recognized species. Both type strains (Z294T and Z443T) shared low 16S rRNA gene sequence similarity, digital DNA-DNA hybridization relatedness and average nucleotide identity values with Georginia satyanarayanai NBRC 107612T, G. subflava JCM 19765T, G. ruanii JCM 15130T and G. thermotolerans DSM 21501T and against each other. The genomic DNA G+C contents of strains Z294T and Z443T were 73.3 and 70 %, respectively. The major cellular fatty acids of strain Z294T were anteiso-C15 : 0, anteiso-C15 : 1 A and C16 : 0, in contrast to anteiso-C15 : 0 and anteiso-C15 : 1 A for strain Z443T. Both type strains (Z294T and Z443T) shared the following common features: glucose, rhamnose and ribose as cell-wall sugars; MK-8(H4) as major menaquinone; alanine, glutamic acid and lysine as cell-wall amino acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified phosphoglycolipid as polar lipids. Comparing the phenotypic and phylogenetic features among the four strains and their related organisms, strains Z294T and Z443T represent two novel species within the genus Georgenia, for which the names Georgenia wutianyii sp. nov. (type strain Z294T=CGMCC 1.16428T=DSM 106344T) and Georgenia yuyongxinii sp. nov. (type strain Z443T=CGMCC 1.16435T=DSM 106174T) are proposed.

Mumia zhuanghuii sp. nov., isolated from the intestinal contents of plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau.

Two Gram-staining-positive, catalase-positive, oxidase-negative, aerobic, non-motile, irregular rod-shaped bacterial strains (Z350T and Z527) were isolated from intestinal contents of plateau pika (Ochotona curzoniae) from the Qinghai-Tibet Plateau, PR China. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Z350T belongs to the genus Mumia (family Nocardioidaceae) but clearly differs from the currently recognized species Mumia xiangluensis DSM 101040T (98.4 % similarity) and Mumia flava DSM 27763T (97.4 %). Strain Z350T had a DNA G+C content of 70.7 mol% and shared 80.4 and 76.7 % average nucleotide identity values and 23.4 and 20.6 % in silico DNA-DNA hybridization relatedness with M. xiangluensis DSM 101040T and M. flava DSM 27763T, respectively. Further phylogenetic analyses based on 497 core genes indicated that our isolates were members of the genus Mumia but separated from all existing genera within the family Nocardioidaceae. The major cellular fatty acids were C18 : 1 ω9c and 10-methyl C18 : 0. The cell wall contained ll-diaminopimelic acid as the diamino acid, and rhamnose, ribose and glucose as whole cell-wall sugars. MK-9(H4) was detected as the major menaquinone. Polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified phospholipid. Based on distinct differences in the genotypic and phenotypic data from the two Mumia species, a novel species, Mumia zhuanghuii sp. nov., is proposed. The type strain is Z350T (=CGMCC 4.7464T=DSM 106288T).