Land application of manure that contains antibiotics and resistant bacteria may facilitate the establishment of an environmental reservoir of antibiotic-resistant microbes, promoting their dissemination into agricultural and natural habitats. The main objective of this study was to search for acquired antibiotic resistance determinants in the gut microbiota of wild boar populations living in natural habitats. Gastrointestinal samples of free-living wild boars were collected in the Zemplén Mountains in Hungary and were characterised by culture-based, metagenomic, and molecular microbiological methods. Bioinformatic analysis of the faecal microbiome of a hunted wild boar from Japan was used for comparative studies. Also, shotgun metagenomic sequencing data of two untreated sewage wastewater samples from North Pest (Hungary) from 2016 were analysed by bioinformatic methods. Minimum spanning tree diagrams for seven-gene MLST profiles of 104 E. coli strains isolated in Europe from wild boars and domestic pigs were generated in Enterobase. In the ileum of a diarrhoeic boar, a dominant E. coli O112ab:H2 strain with intermediate resistance to gentamicin, tobramycin, and amikacin was identified, displaying sequence type ST388 and harbouring the EAST1 toxin astA gene. Metagenomic analyses of the colon and rectum digesta revealed the presence of the tetQ, tetW, tetO, and mefA antibiotic resistance genes that were also detected in the gut microbiome of four other wild boars from the mountains. Furthermore, the tetQ and cfxA genes were identified in the faecal microbiome of a hunted wild boar from Japan. The gastrointestinal microbiota of the free-living wild boars examined in this study carried acquired antibiotic resistance determinants that are highly prevalent among domestic livestock populations.

A significant threat to public health is presented by antibiotic-resistant strains of bacteria, selective pressure on which results from antibiotic use. Colistin is an antibiotic commonly used in veterinary medicine, but also one of last resort in human medicine. Since the 2015 discovery in China of the mcr-1 gene encoding colistin resistance in Enterobacteriaceae, other countries have noted its presence. This study was to find the mcr-1 gene prevalence in E. coli isolated from poultry slaughtered in Poland. Cloacal swabs were taken from December 2017 to October 2018 from broiler chickens in three regions. The samples (n = 158) were grouped as flocks treated with colistin sulphate (n = 87) and those not treated (n = 71). Resistance to antimicrobials commonly used in poultry was evaluated by minimum inhibitory concentration. The presence of the mcr-1 gene was confirmed by PCR. Isolates containing the mcr-1 gene were yielded by 11.27% of the samples from not treated flocks and 19.54% of those from treated flocks, but no statistically significant difference in the prevalence of the gene was seen between the groups. The results clearly preclude intensification of selective pressure for colistin resistance due to colistin sulphate treatment because they show that the avian gastrointestinal tract was already inhabited by colistin-resistant E. coli by the time the chickens came to the poultry house.

OBJECTIVE To determine the effects of oral omeprazole administration on the fecal and gastric microbiota of healthy adult horses. ANIMALS 12 healthy adult research horses. PROCEDURES Horses were randomly assigned to receive omeprazole paste (4 mg/kg, PO, q 24 h) or a sham (control) treatment (tap water [20 mL, PO, q 24 h]) for 28 days. Fecal and gastric fluid samples were collected prior to the first treatment (day 0), and on days 7, 28, 35, and 56. Sample DNA was extracted, and bacterial 16S rRNA gene sequences were amplified and sequenced to characterize α and β diversity and differential expression of the fecal and gastric microbiota. Data were analyzed by visual examination and by statistical methods. RESULTS Composition and diversity of the fecal microbiota did not differ significantly between treatment groups or over time. Substantial variation in gastric fluid results within groups and over time precluded meaningful interpretation of the microbiota in those samples. CONCLUSIONS AND CLINICAL RELEVANCE Results supported that omeprazole administration had no effect on fecal microbiota composition and diversity in this group of healthy adult horses. Small sample size limited power to detect a difference if one existed; however, qualitative graphic examination supported that any difference would likely have been small and of limited clinical importance. Adequate data to evaluate potential effects on the gastric microbiota were not obtained. Investigations are needed to determine the effects of omeprazole in horses with systemic disease or horses receiving other medical treatments.

Sixteen IgA-deficient German Shepherd Dogs with small intestinal bacterial overgrowth were randomized into 2 groups. One group was fed a chicken-based kibble diet; the other was fed the same diet, but with 1% fructo-oligosaccharides supplemented at the expense of cornstarch. After being exposed to the diets for 46 to 51 days, the group that ate the supplemented diet had significantly (P = 0.04) fewer aerobic/facultative anaerobic bacterial colony-forming units in fluid from the duodenum/proximal part of the jejunum, as well as in the duodenal mucosa. We could not detect significant differences in the species of bacteria found in the intestine of these 2 groups of dogs. We conclude that at least some dietary carbohydrates can affect small intestinal bacterial populations in dogs with small intestinal bacterial overgrowth.

To assess the role of enterotoxigenic (ETEC), verotoxigenic (VTEC), and necrotoxigenic (NTEC) Escherichia coli in cattle with diarrhea, 1,524 colonies of E coli isolated from 197 calves with diarrhea and from 112 healthy controls were investigated for production of heat-labile and heat-stable enterotoxins, verotoxins, and cytotoxic necrotizing factors (CNF1 and CNF2). The ETEC were isolated from only 2 (1%) calves with diarrhea and from 5 (4%) healthy controls. In contrast, VTEC and NTEC that produced CNF2 were frequently identified. The VTEC were isolated from 18 (9%) calves with diarrhea and from 21 (19%) healthy cattle (P < 0.05), whereas NTEC that produced CNF2 were detected in 39 (20%) ill calves and in 38 (34%) controls (P < 0.01). Therefore, VTEC and NTEC that produced CNF2 were isolated significantly more frequently from healthy than diseased calves. Serogroups to which VTEC belonged differed considerably from the O groups involved with NTEC. Although, VTEC belonged to 18 serogroups, only 4 (O26, O103, O113, and O157) accounted for 56% (25 of 45) of verotoxigenic strains. The NTEC that produced CNF2 belonged to 26 serogroups; however, 64% (69 of 108) were from 6 serogroups (O1, O3, O15, O55, O88, and O123). Our results are compatible with cattle being a reservoir of VTEC that are pathogenic for human beings and with ETEC being an unusual cause of bovine colibacillosis in Galicia (northwestern Spain). Furthermore, results of this study indicate that VTEC and NTEC that produced CNF2 may be part of the normal intestinal flora of cattle.

The effect of intestinal microflora on digestible energy (DE) value and fiber digestion was studied in single-comb White Leghorn chickens fed a low-fiber diet (experiment 1) or a high-fiber diet with low or adequate metabolizable energy (ME) value (experiment 2). Fecal energy excretion was calculated from the difference between total energy excretion in urinary and fecal droppings and urinary energy excretion, which was estimated from the energy values for individual urinary nitrogenous compounds extracted with Li2CO3. When the birds were fed the low-fiber diet, no differences in growth, DE, or ME were observed between germ-free and conventional environments. Of birds fed the high-fiber diet, growth of those in the conventional environment was similar to that of the birds in the germ-free environment at the adequate ME value, whereas birds in the conventional environment grew faster than the birds in the germ-free environment at the low ME value. Changes in observed dietary ME values of the high-fiber diets, being higher in birds in the conventional environment than in birds in the germ-free environment (experiment 2), were almost entirely accounted for by those in dietary DE values, most of which was contributed by crude fiber digestion. It was concluded, therefore, that by means of fiber digestion, the intestinal microflora may benefit the host bird by supplying extra energy, which would result in growth promotion, particularly when the bird is deficient in energy.

The goal of this study was to explore and describe fecal microbiota of captive and wild bobcats (Lynx rufus) and compare the results to those of domestic cats (Felis catus). Fecal samples from 27 bobcats (8 wild, 19 zoo-kept) were used for novel bacterial deoxyribonucleic acid (DNA) identification using next-generation sequencing of the V4 region of the bacterial 16S ribosomal ribonucleic acid (rRNA) gene, analyzed by Illumina sequencing, and then compared to data obtained from a colony of 10 domestic cats. In this study, the microbiota of both species was dominated by Firmicutes, followed by Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. When compared, fecal samples from bobcats harbored more Proteobacteria and Actinobacteria than fecal samples from domestic cats. There was a remarkable inter-bobcat variation in the relative abundances of the main bacterial genera. There were no significant differences, however, between the main phyla of the microbiota of the wild and domestic bobcats. Proteobacteria in wild bobcats (P = 0.079) and Firmicutes in zoo-kept bobcats (P = 0.079) approached significance. There were no differences in predominant genera between wild and captive bobcats. The results of this study showed that there are notable differences in fecal bacterial communities between domestic cats and both captive and wild bobcats. The lack of significant differences in bacterial communities between wild and zoo-kept bobcats suggests that the varied diet provided for these felids can result in a fecal microbiota resembling that generated by a wild diet.

OBJECTIVE To determine effects of restriction feeding of a moderate-protein, high-fiber diet on loss of body weight (BW), voluntary physical activity, body composition, and fecal microbiota of overweight cats. ANIMALS 8 neutered male adult cats. PROCEDURES After BW maintenance for 4 weeks (week 0 = last week of baseline period), cats were fed to lose approximately 1.5% of BW/wk for 18 weeks. Food intake (daily), BW (twice per week), body condition score (weekly), body composition (every 4 weeks), serum biochemical analysis (weeks 0, 1, 2, 4, 8, 12, and 16), physical activity (every 6 weeks), and fecal microbiota (weeks 0, 1, 2, 4, 8, 12, and 16) were assessed. RESULTS BW, body condition score, serum triglyceride concentration, and body fat mass and percentage decreased significantly over time. Lean mass decreased significantly at weeks 12 and 16. Energy required to maintain BW was 14% less than National Research Council estimates for overweight cats and 16% more than resting energy requirement estimates. Energy required for weight loss was 11% more, 6% less, and 16% less than American Animal Hospital Association recommendations for weight loss (80% of resting energy requirement) at weeks 1 through 4, 5 through 8, and 9 through 18, respectively. Relative abundance of Actinobacteria increased and Bacteroidetes decreased with weight loss. CONCLUSIONS AND CLINICAL RELEVANCE Restricted feeding of a moderate-protein, high-fiber diet appeared to be a safe and effective means for weight loss in cats. Energy requirements for neutered cats may be overestimated and should be reconsidered.

OBJECTIVE To determine effects of in ovo administration of a probiotic on development of the intestinal microbiota of 2 genetic lineages (modern and heritage) of chickens. SAMPLE 10 newly hatched chicks and 40 fertile eggs to determine intestinal microbiota at hatch, 900 fertile eggs to determine effects of probiotic on hatchability, and 1,560 chicks from treated or control eggs. PROCEDURES A probiotic competitive-exclusion product derived from adult microbiota was administered in ovo to fertile eggs of both genetic lineages. Cecal contents and tissues were collected from embryos, newly hatched chicks, and chicks. A PCR assay was used to detect bacteria present within the cecum of newly hatched chicks. Fluorescence in situ hybridization and vitality staining were used to detect viable bacteria within intestines of embryos. The intestinal microbiota was assessed by use of 16S pyrosequencing. RESULTS Microscopic evaluation of embryonic cecal contents and tissues subjected to differential staining techniques revealed viable bacteria in low numbers. Development of the intestinal microbiota of broiler chicks of both genetic lineages was enhanced by in ovo administration of adult microbiota. Although the treatment increased diversity and affected composition of the microbiota of chicks, most bacterial species present in the probiotic were transient colonizers. However, the treatment decreased the abundance of undesirable bacterial species within heritage lineage chicks. CONCLUSIONS AND CLINICAL RELEVANCE In ovo inoculation of a probiotic competitive-exclusion product derived from adult microbiota may be a viable method of managing development of the microbiota and reducing the prevalence of pathogenic bacteria in chickens.

Proliferative enteropathy is an important enteric disease caused by Lawsonia intracellularis. A wide range of host species can be infected by the same bacterium, yet the clinico-pathologic features among these hosts remains almost identical. The disease has been recognized regularly among ratites, but not in other avian families, such as galliforms, even though these suffer uncharacterized enteric conditions. Fresh ileum-colon contents were obtained from 228, 3- to 8-week-old chickens with enteric disease, kept at 14 large commercial farms in the southern USA. DNA was extracted from each sample and subjected to polymerase chain reactions (PCR) with primers specific to eubacterial DNA, L. intracellularis, and Bilophila wadsworthia. All chicken samples were positive for eubacterial DNA, 29 chickens (13%) were positive for B. wadsworthia DNA, and none were positive for L. intracellularis DNA. Given the ubiquitous nature of L. intracellularis, we consider it likely that some avian families do not carry the necessary mechanism for L. intracellularis viability. Bilophila wadsworthia appears to be a consistent member of the colonic flora of some host animals. Neither bacterium appears to be associated with malabsorption syndromes in chickens.