Molecular ecological analysis of dietary and antibiotic-induced alterations of the mouse intestinal microbiota

Impact of intestinal microbiota on metabolic toxicity and potential detoxification of amygdalin

Amygdalin (Amy) is metabolized into cyanide in vivo, which may lead to fatal poisoning after oral administration. The defense mechanisms against toxic cyanide have not yet been adequately studied. In this study, comparative toxicokinetics study of Amy was performed in normal and pseudo germ-free rats. The efficiency of cyanide release was significant higher in normal group when given a single oral dose of 440 mg/kg (50% median lethal dose). Thiocyanate, the detoxification metabolite, was firstly detected in feces, caecum, and intestinal microbiota incubation enzymic system. The results suggest intestinal microbiota is involved in bidirectional regulation of toxicity and detoxification of Amy. We further identified the species related to cyanogenesis of Amy with metagenomic sequencing, such as Bifidobacterium pseudolongum, Marvinbryantia formatexigens, and Bacteroides fragilis. Functional analysis of microbiota reveals the detoxification potential of intestinal microbiota for cyanide. Sulfurtransferase superfamily, such as rhodanese, considered as main detoxification enzymes for cyanide, are largely found in Coriobacteriaceae bacterium, Butyricicoccus porcorum, Akkermansia muciniphila, etc. Besides, cyanoamino acid metabolism pathway dominated by Escherichia coli may contribute to the detoxification metabolism of cyanide. In summary, intestinal microbiota may be the first line of defense against the toxicity induced by Amy.

Systematic Review and Meta-analysis: Changes of Gut Microbiota before and after Menopause

Objective. To systematically evaluate the differences in intestinal flora before and after menopause. To provide a possible mechanism for perimenopausal syndrome and provide a basis for probiotics as adjuvant therapy. Methods. MEDLINE, EMBASE, Web of Science, Cochrane Central Register of Controlled Trials (CENTRAL), CNKI, Wanfang, and VIP databases were searched. The included studies were case-control studies. Results. Three case-control studies were included, with a total of 156 people. At the phylum level, there were no differences between premenopausal and postmenopausal women. At the genus level, the relative abundances of A. odoratum and B. cholerae were higher in postmenopausal women than in premenopausal women, with no differences among other genera. The Shannon diversity index increased after menopause, but no differences were found. Only one study found a positive association of estradiol with Gammaproteobacteria and Myxococcales and a negative association with Prevotellaceae. Conclusions. On the basis of previous studies, it was found that there was no significant difference at the phylum level between postmenopausal women and premenopausal women, but Odoribacter and Bilophila increased at the genus level in postmenopausal women. The class of Gammaproteobacteria may be positively correlated with estradiol. Limited by the number of included studies, more high-quality clinical studies are needed for validation.

Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota

Nutrient supply to ecosystems has major effects on ecological diversity, but it is unclear to what degree the shape of this relationship is general versus dependent on the specific environment or community. Although the diet composition in terms of the source or proportions of different nutrient types is known to affect gut microbiota composition, the relationship between the quantity of nutrients supplied and the abundance and diversity of the intestinal microbial community remains to be elucidated. Here, we address this relationship using replicate populations of Drosophila melanogaster maintained over multiple generations on three diets differing in the concentration of yeast (the only source of most nutrients). While a 6.5-fold increase in yeast concentration led to a 100-fold increase in the total abundance of gut microbes, it caused a major decrease in their alpha diversity (by 45-60% depending on the diversity measure). This was accompanied by only minor shifts in the taxonomic affiliation of the most common operational taxonomic units (OTUs). Thus, nutrient concentration in host diet mediates a strong negative relationship between the nutrient abundance and microbial diversity in the Drosophila gut ecosystem.

Gut microbes limit growth in house sparrow nestlings (Passer domesticus) but not through limitations in digestive capacity

Recent research often lauds the services and beneficial effects of host‐associated microbes on animals. However, hosting these microbes may come at a cost. For example, germ‐free and antibiotic‐treated birds generally grow faster than their conventional counterparts. In the wild, juvenile body size is correlated with survival, so hosting a microbiota may incur a fitness cost. Avian altricial nestlings represent an interesting study system in which to investigate these interactions, given that they exhibit the fastest growth rates among vertebrates, and growth is limited by their digestive capacity. We investigated whether reduction and restructuring of the microbiota by antibiotic treatment would: (i) increase growth and food conversion efficiency in nestling house sparrows (Passer domesticus); (ii) alter aspects of gut anatomy or function (particularly activities of digestive carbohydrases and their regulation in response to dietary change); and (iii) whether there were correlations between relative abundances of microbial taxa, digestive function and nestling growth. Antibiotic treatment significantly increased growth and food conversion efficiency in nestlings. Antibiotics did not alter aspects of gut anatomy that we considered but depressed intestinal maltase activity. There were no significant correlations between abundances of microbial taxa and aspects of host physiology. Overall, we conclude that microbial‐induced growth limitation in developing birds is not driven by interactions with digestive capacity. Rather, decreased energetic and material costs of immune function or beneficial effects from microbes enriched under antibiotic treatment may underlie these effects. Understanding the costs and tradeoffs of hosting gut microbial communities represents an avenue of future research.

Dietary High Fluorine Alters Intestinal Microbiota in Broiler Chickens

This study investigated the effects of dietary high fluorine on ileal and cecal microbiota in broiler chickens. Two hundred eighty 1-day-old broiler chickens were randomly assigned to four groups and raised for 42 days. The control group was fed a corn-soybean basal diet (fluorine 22.6 mg/kg). The other three groups were fed the same basal diet, but supplemented with 400, 800, and 1200 mg/kg fluorine (high fluorine groups I, II, and III), administered in the form of sodium fluoride. The microbiota of ileal and cecal digesta was assessed with plate counts and polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE). It was found that, compared with those in the control group, the counts of Lactobacillus spp. and Bifidobacterium spp. were markedly decreased (P < 0.01 or P < 0.05), whereas the counts of Escherichia coli and Enterococcus spp. were significantly increased (P < 0.01 or P < 0.05) in the high fluorine groups II and III. PCR-DGGE analysis showed that the number of DGGE bands, similarity, and Shannon index of ileal and cecal bacteria were markedly reduced in the high fluorine groups II and III from 21 to 42 days. Sequencing analysis revealed that the composition of the intestinal microbiota was altered in the high fluorine groups. In conclusion, dietary fluorine in the range of 800-1200 mg/kg obviously altered the bacterial counts, and the diversity and composition of intestinal microbiota in broiler chickens, a finding which implies that dietary high fluorine can disrupt the natural balance and structure of the intestinal microbiota.

Novel and disruptive biological strategies for resolving gut health challenges in monogastric food animal production

Use of feed antibiotics as growth promoters for control of pathogens associated with monogastric food animal morbidity and mortality has contributed to the development of antimicrobial resistance, which has now become a threat to public health on a global scale. Presently, a number of alternative feed additives have been developed and are divided into two major categories, including 1) the ones that are supposed to directly and indirectly control pathogenic bacterial proliferation; and 2) the other ones that are intended to up-regulate host gut mucosal trophic growth, whole body growth performance and active immunity. A thorough review of literature reports reveal that efficacy responses of current alternative feed additives in replacing feed antibiotics to improve performances and gut health are generally inconsistent dependent upon experimental conditions. Current alternative feed additives typically have no direct detoxification effects on endotoxin lipopolysaccharides (LPS) and this is likely the major reason that their effects are limited. It is now understood that pathogenic bacteria mediate their negative effects largely through LPS interactions with toll-like receptor 4, causing immune responses and infectious diseases. Therefore, disruptive biological strategies and a novel and new generation of feed additives need to be developed to replace feed antibiotic growth promoters and to directly and effectively detoxify the endotoxin LPS and improve gut health and performance in monogastric food animals.

Alleviation of high fat diet-induced obesity by oligofructose in gnotobiotic mice is independent of presence of Bifidobacterium longum

Scope

Diet‐induced obesity is associated with changes in the gut microbiota and low‐grade inflammation. Oligofructose was reported to ameliorate high fat diet‐induced metabolic disorders in mice by restoring the number of intestinal bifidobacteria. However, this has not been experimentally demonstrated.

Methods and results

We fed conventional mice, germfree mice, mice associated with a simplified human gut microbiota composed of eight bacterial species including Bifidobacterium longum (SIHUMI), and mice associated with SIHUMI without B. longum a low fat diet (LFD), a high fat diet (HFD), or a HFD containing 10% oligofructose (HFD + OFS) for five weeks. We assessed body composition, bacterial cell numbers and metabolites, markers of inflammation, and gut permeability. Conventional mice fed HFD or HFD + OFS did not differ in body weight gain and glucose tolerance. The gnotobiotic mouse groups fed LFD or HFD + OFS gained less body weight and body fat, and displayed an improved glucose tolerance compared with mice fed HFD. These differences were not affected by the presence of B. longum. Mice fed HFD showed no signs of inflammation or increased intestinal permeability.

Conclusion

The ability of oligofructose to reduce obesity and to improve glucose tolerance in gnotobiotic mice fed HFD was independent of the presence of B. longum.

Tumor grafting induces changes of gut microbiota in athymic nude mice in the presence and absence of medicinal Gynostemma saponins

Recent findings have revealed that gut microbiota plays a substantial role in modulating diseases such as autism, rheumatoid arthritis, allergies, and cancer that occur at sites distant to the gut. Athymic nude mice have been employed for tumorigenic research for decades; however, the relationships between the gut microbiome and host's response in drug treatment to the grafted tumors have not been explored. In this study, we analyzed the fecal microbiome of nonxenograft and xenograft nude mice treated with phytosaponins from a popular medicinal plant, Gynostemma pentaphyllum (Gp). Analysis of enterobacterial repetitive intergenic consensus (ERIC)-PCR data showed that the microbiota profile of xenograft mice departed from that of the nonxenograft mice. After ten days of treatment with Gp saponins (GpS), the microbiota of the treated mice was closer to the microbiota at Day 0 before the implantation of the tumor. Data obtained from 16S pyrosequencing of fecal samples reiterates the differences in microbiome between the nonxenograft and xenograft mice. GpS markedly increased the relative abundance of Clostridium cocleatum and Bacteroides acidifaciens, for which the beneficial effects on the host have been well documented. This study, for the first time, characterizes the properties of gut microbiome in nude mice responding to tumor implant and drug treatment. We also demonstrate that dietary saponins such as GpS can potentially regulate the gut microbial ecosystem by increasing the number of symbionts. Interestingly, this regulation of the gut ecosystem might, at least in part, be responsible for or contribute to the anticancer effect of GpS.

Toxicological effects of dietary nickel chloride on intestinal microbiota

This study was designed to evaluate the toxicological effect of dietary nickel chloride (NiCl2) on the counts of intestinal bacteria and diversity of microorganisms in broilers. Plate counting and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assays were used. A total of 240 one-day-old avian broilers chicks were divided into four equal groups and kept on corn-soybean basal diet along with supplementation of 0, 300, 600 and 900 mg/kg NiCl2 for 42 days. Samples were taken at 21 and 42 days of age during the experiment. The bacterial count results showed that dietary NiCl2 in the range of 300 to 900 mg/kg decreased the counts of Bifidobacterium spp. and Lactobacillus, increased Escherichia coli (E. coli) and Enterococcus spp. in the ileum and cecum. PCR-DGGE analysis showed that bacterial band numbers, profile similarity, and the Shannon index of the ileum and cecum were all decreased in the 300, 600, and 900 mg/kg groups at 21 and 42 days of age. In conclusion, dietary NiCl2 affected the amount and diversity of intestinal microbiota in the ileum and cecum of broilers. This finding implies that NiCl2 has toxicological effect on the intestinal ecosystem and, possibly functions.

Xanthohumol improved cognitive flexibility in young mice

The protein palmitoylation cycle has been shown to be important for protein signaling and synaptic plasticity. Data from our lab showed a change in the palmitoylation status of certain proteins with age. A greater percentage of the NMDA receptor subunits GluN2A and GluN2B, along with Fyn and PSD95 proteins, were palmitoylated in the old mice. The higher level of protein palmitoylation was also associated with poorer learning scores. Xanthohumol is a prenylated flavonoid that has been shown to increase beta-oxidation in the livers of rodents, decreasing circulating free fatty acids in the serum. What is not known is whether the application of xanthohumol could influence the palmitoylation status of proteins. In this study, young and old mice were fed a diet supplemented with xanthohumol for 8 weeks. Spatial memory was assessed with the Morris water maze and protein palmitoylation quantified. The young xanthohumol-treated mice showed a significant improvement in cognitive flexibility. However, this appeared to be associated with the young control mice, on a defined, phytoestrogen-deficient diet, performing as poorly as the old mice and xanthohumol reversing this effect. The old mice receiving xanthohumol did not significantly improve their learning scores. Xanthohumol treatment was unable to affect the palmitoylation of NMDA receptor subunits and associated proteins assessed in this study. This evidence suggests that xanthohumol may play a role in improving cognitive flexability in young animals, but it appears to be ineffective in adjusting the palmitoylation status of neuronal proteins in aged individuals.

Gut microbial diversity in rat model induced by rhubarb

Rhubarb is often used to establish chronic diarrhea and spleen (Pi)-deficiency syndrome animal models in China. In this study, we utilized the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) method to detect changes in bacterial diversity in feces and the bowel mucosa associated with this model. Total microbial genomic DNA from the small bowel (duodenum, jejunum, and ileum), large bowel (proximal colon, distal colon, and rectum), cecum, and feces of normal and rhubarb-exposed rats were used as templates for the ERIC-PCR analysis. We found that the fecal microbial composition did not correspond to the bowel bacteria mix. More bacterial diversity was observed in the ileum of rhubarb-exposed rats (P<0.05). Furthermore, a 380 bp product was found to be increased in rhubarb-exposed rats both in faces and the bowel mucosa. The product was cloned and sequenced and showed high similarity with regions of the Bacteroides genome. AS a result of discriminant analysis with the SPSS software, the Canonical Discriminant Function Formulae for model rats was established.

Isolation and gut microbiota modulation of antibiotic-resistant probiotics from human feces

Antibiotic-resistant probiotics may be advantageous for antibiotic-induced gut microbiota imbalance. In this article, we aimed to isolate antibiotic-resistant bacteria as potential probiotics. Feces from 3 healthy adults and 2 infants were used to isolate the antibiotic-resistant bacteria. Then we established gut microbiota imbalance mice model by antibiotics treatment and used it to assess the effect of the probiotics. Finally, we identified 8 isolates, and 6 of them were used as probiotics cocktail. Number of anaerobe, lactobacilli, and Bifidobacterium in feces were higher in the probiotic group (9.47±0.35 log10CFU/g, 8.74±0.18 log10CFU/g, 7.24±0.38 log10CFU/g, respectively) compared with model group (P<0.05). Richness and diversity index of probiotic group (19.79±0.29 and 2.95±0.06, respectively) were larger than model group (P<0.05). Diarrhea and mucosal edema had been alleviated during probiotic treatment. Our results validated that bacteriotherapy was available to treat gut microbiota imbalance.

Salecan diet increases short chain fatty acids and enriches beneficial microbiota in the mouse cecum

Salecan, a linear extracellular polysaccharide consisting of β-(1,3)-D-glucan, has potential applications in the food industry due to its excellent toxicological profile and rheological properties. The aim of the present study was to evaluate the effects of dietary supplementation with 8% Salecan on the gastrointestinal microbiota in mice. In the Salecan group, the following significant differences (p<0.05) from the cellulose group were found: increased body weight gain, greater mass of cecum and cecal contents, and higher butyrate concentrations in the cecal and colonic contents at wk 4. Moreover, populations of Lactobacillus and Bifidobacterium increased 3- and 6-fold, respectively, in the cecal contents of mice consuming Salecan. These results suggest that the dietary incorporation of Salecan, by providing SCFAs and increasing beneficial microbiota, may be beneficial in improving gastrointestinal health, and have relevance to the use of Salecan as a dietary supplement for human consumption.

Supplementation of diets with bovine colostrum influences immune function in dogs

While the need for colostrum in neonates is well established, the systemic effect of feeding bovine colostrum (BC) to adult humans is gaining increasing attention. However, no systematic studies evaluating the immunomodulatory effect of BC in dogs have been reported. The aim of the present study was to evaluate the immunomodulatory effect of dietary supplementation of BC in dogs. The study was conducted in two phases: pre-test (8 weeks) and test (40 weeks), with twenty-four dogs (mean age 2.5 years) randomised into two groups. In the 'pre-test' phase, both groups were fed a nutritionally complete diet. At the end of the 'pre-test' phase, all dogs received a canine distemper virus (CDV) vaccine, and dogs in the 'test group' were switched to a diet supplemented with 0.1% spray-dried BC. Response to the CDV vaccine was evaluated by measuring vaccine-specific plasma IgG levels. Gut-associated lymphoid tissue response was assessed by measuring faecal IgA levels. Gut microbiota were evaluated by the temporal temperature gel electrophoresis methodology. Dogs fed the BC-supplemented diet demonstrated a significantly higher vaccine response and higher levels of faecal IgA when compared with the control group. Supplementing diets with BC also resulted in significantly increased gut microbiota diversity and stability in the test group. In conclusion, diets supplemented with BC significantly influence immune response in dogs.

Antibiotics in early life alter the murine colonic microbiome and adiposity

Antibiotics administered in low doses have been widely used as growth promoters in the agricultural industry since the 1950s, yet the mechanisms for this effect are unclear. Because antimicrobial agents of different classes and varying activity are effective across several vertebrate species, we proposed that such subtherapeutic administration alters the population structure of the gut microbiome as well as its metabolic capabilities. We generated a model of adiposity by giving subtherapeutic antibiotic therapy to young mice and evaluated changes in the composition and capabilities of the gut microbiome. Administration of subtherapeutic antibiotic therapy increased adiposity in young mice and increased hormone levels related to metabolism. We observed substantial taxonomic changes in the microbiome, changes in copies of key genes involved in the metabolism of carbohydrates to short-chain fatty acids, increases in colonic short-chain fatty acid levels, and alterations in the regulation of hepatic metabolism of lipids and cholesterol. In this model, we demonstrate the alteration of early-life murine metabolic homeostasis through antibiotic manipulation.

Reduction of soybean meal non-starch polysaccharides and α-galactosides by solid-state fermentation using cellulolytic bacteria obtained from different environments

Soybean meal (SBM) is an important protein source in animal feed. However, the levels of SBM inclusion are restricted in some animal species by the presence of antinutritional factors (ANFs), including non-starch polysaccharides (NSPs) and α-galactosides (GOSs). The aim of this study was to reduce the soybean meal NSPs and GOSs by solid-state fermentation (SSF) using a combination of cellulolytic bacteria isolated from different environments (termites, earthworms, corn silage and bovine ruminal content). To analyse the key enzymatic activities, the isolates were grown in minimal media containing NSPs extracted from SBM. The selected bacterial strains belonged to the genera Streptomyces, Cohnella and Cellulosimicrobium. SSF resulted in a reduction of nearly 24% in the total NSPs, 83% of stachyose and 69% of raffinose and an increase in the protein content. These results suggest that cellulolytic bacteria-based SSF processing facilitates SBM nutritional improvement. In addition, the use of fermented SBM in animal diets can be recommended.

Molecular analysis of bacterial microbiota associated with oysters (Crassostrea gigas and Crassostrea corteziensis) in different growth phases at two cultivation sites

Microbiota presumably plays an essential role in inhibiting pathogen colonization and in the maintenance of health in oysters, but limited data exist concerning their different growth phases and conditions. We analyzed the bacterial microbiota composition of two commercial oysters: Crassostrea gigas and Crassostrea corteziensis. Differences in microbiota were assayed in three growth phases: post-larvae at the hatchery, juvenile, and adult at two grow-out cultivation sites. Variations in the microbiota were assessed by PCR analysis of the 16S rRNA gene in DNA extracted from depurated oysters. Restriction fragment length polymorphism (RFLP) profiles were studied using Dice's similarity coefficient (Cs) and statistical principal component analysis (PCA). The microbiota composition was determined by sequencing temperature gradient gel electrophoresis (TGGE) bands. The RFLP analysis of post-larvae revealed homology in the microbiota of both oyster species (Cs > 88 %). Dice and PCA analyses of C. corteziensis but not C. gigas showed differences in the microbiota according to the cultivation sites. The sequencing analysis revealed low bacterial diversity (primarily β-Proteobacteria, Firmicutes, and Spirochaetes), with Burkholderia cepacia being the most abundant bacteria in both oyster species. This study provides the first description of the microbiota in C. corteziensis, which was shown to be influenced by cultivation site conditions. During early growth, we observed that B. cepacia colonized and remained strongly associated with the two oysters, probably in a symbiotic host-bacteria relationship. This association was maintained in the three growth phases and was not altered by environmental conditions or the management of the oysters at the grow-out site.

Development and genetic influence of the rectal bacterial flora of newborn calves

The aim of the study was to investigate a dynamic change in the rectal flora of calves as well as to study a genetic influence on the intestinal microflora of calves. The bacterial community of fecal samples from calves was examined by PCR single strand conformation polymorphism (PCR-SSCP) in two independent studies. In study one 14 newborn calves of the same farm were examined. Sampling was conducted directly after delivery (meconium) and after 6 h, 12 h, 24 h, 48 h, 3 d, 7 d, 14 d and 42 d of life. In study two 6 twin calves and their coresident of the same age and farm were analysed in order to study for the first time whether genetic predisposition of the host may influence the fecal microflora. All calves were weaned directly after delivery and received pumped colostrum without direct contact to other farm animals. After delivery and during the first 12h of life the SSCP profiles were simple, but became more complex since the bacterial diversity increased with time in all calves. It became obvious that the intra-individual band-pattern similarity decreased over time and inter-individual similarity was low. The analysis of fecal samples from twin calves revealed higher similarity in SSCP profiles for twins compared to their coresident indicating that the individual microflora might be genetically or epigenetically influenced. The insight that there are several conformities between intestinal microfloras of healthy calves and that there might be genetic influence on the fecal flora could help to prevent diarrhoeal diseases in the future.

Effect of recycled litter on immune cells in the cecal tonsils of chickens

This experiment was conducted to study selected aspects of the gut immune response in broiler chicks reared on fresh or recycled litter that were fed diets with and without subtherapeutic antibiotic supplementation. All of the chicks were reared in pens that contained either fresh pine shavings (fresh litter) or litter that was recycled for 3 consecutive flocks (recycled litter). The experiment was a 2 × 2 factorial arrangement of treatments with 4 replicate pens (n = 4) per treatment. At 10 and 35 d of age, the cecal tonsils were analyzed for intestinal immune measurements. The cecal tonsils of birds reared on recycled litter had increased IL-1 mRNA (P < 0.01) and a lower percentage of CD4(+)CD25(+) cells at 10 and 35 d of age when compared with those of chicks reared on fresh litter. Birds fed diets supplemented with bacitracin had a reduction in CD4(+) cells (P = 0.01) at 10 d of age when compared with that of chicks that were not fed the antibiotic. The combination of bacitracin supplementation and fresh litter resulted in an approximate 10-fold increase in IL-10 mRNA (P = 0.01) at 10 d of age when compared with that of the unsupplemented chicks in fresh litter. Among those chicks that were not supplemented with bacitracin, the recycled-litter treatment resulted in 25-fold (P = 0.01) and 39-fold (P = 0.02) higher IL-4 mRNA levels at 10 and 35 d of age, respectively, when compared with those of the chicks reared on fresh litter. In conclusion, the intestinal immune response of birds reared on recycled litter is skewed toward an inflammatory response, whereas the fresh litter treatment was skewed toward an anti-inflammatory response. Bacitracin supplementation did not interact with the litter type to alter IL-1 mRNA levels in cecal tonsils, suggesting the low efficiency of bacitracin in alleviating the inflammatory response induced by recycled litter.

Influence of antimicrobial feed additives on broiler commensal posthatch gut microbiota development and performance

The effects of avilamycin, zinc bacitracin, and flavophospholipol on broiler gut microbial community colonization and bird performance in the first 17 days posthatch were investigated. Significant differences in gut microbiota associated with gut section, dietary treatment, and age were identified by terminal restriction fragment length polymorphism (T-RFLP), although no performance-related differences between dietary treatments were detected. Similar age-related shifts in the gut microbiota were identified regardless of diet but varied between the ilea and ceca. Interbird variabilities in ileal bacterial communities were reduced (3 to 7 days posthatch) in chicks fed with feed containing antimicrobial agents. Avilamycin and flavophospholipol had the most consistent effect on gut microbial communities. Operational taxonomic units (OTU) linked to changes in gut microbiota in birds on antimicrobial-supplemented diets were characterized and identified. Some OTUs could be identified to the species level; however, the majority could be only tentatively classified to the genus, family, order, or domain level. OTUs 140 to 146 (Lachnospiraceae), OTU 186/188 (Lactobacillus johnsonii), OTU 220 (Lachnospiraceae), OTUs 284 to 288 (unclassified bacterial spp. or Ruminococcaceae), OTU 296/298 (unclassified bacterium or Clostridiales), and OTU 480/482 (Oxalobacteraceae) were less prevalent in the guts of chicks fed antimicrobial-supplemented diets. OTU 178/180 (Lactobacillus crispatus), OTU 152 (Lactobacillus reuteri or unclassified Clostridiales), OTU 198/200 (Subdoligranulum spp.), and OTU 490/492 (unclassified bacterium or Enterobacteriaceae) were less prevalent in the gut of chicks raised on the antimicrobial-free diet. The identification of key bacterial species influenced by antimicrobial-supplemented feed immediately posthatch may assist in the formulation of diets that facilitate beneficial gut microbial colonization and, hence, the development of alternatives to current antimicrobial agents in feed for sustainable poultry production.

Characterisation and response of intestinal microflora and mucins to manno-oligosaccharide and antibiotic supplementation in broiler chickens

1. An experiment was conducted to characterise and evaluate, in comparison to zinc bacitracin (ZnB), the response of intestinal microflora and mucins to manno-oligosacchares (MOS, Bio-MOS(R), Alltech Biotechnology, Nicholasville, Kentucky, USA). 2. Supplementation of MOS and ZnB selectively increased the intensity of sulphomucins. As revealed by the plate culture method, MOS accelerated the maturation of gut microflora by promoting the growth of lactobacilli in the ileal mucosa and vice versa on ileal and caecal clostridia. Unlike MOS, ZnB suppressed the growth of intestinal bacteria, especially those of lactobacilli and clostridia. Use of T-RFLP further revealed that MOS increased the diversity of lactobacilli in the ileum and ileal mucosa but the opposite was observed for ZnB. It also appears that MOS and ZnB possessed a common property in differentially favouring the growth of certain Lactobacillus species. There was also evidence to show that both MOS and ZnB also increased the homogeneity of the gut microflora, possibly through the regulation of the overall gut bacterial communities. 3. Improvement in intestinal microbial homogeneity and mucin synthesis, coupled with the differential selections for certain specific beneficial bacterial species, may ultimately be proven to be the target mechanisms in the search for more effective alternatives to antibiotics.

Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch

The composition and dynamics of the gastrointestinal bacterial communities in birds is determined by both host-specific and environmental exposure factors yet these are poorly understood. We selected the zebra finch, Taeniopygia guttata, as the host species to examine the diversity and temporal stability of the faecal microflora in a bird, owing to its importance as a model organism in avian ecology, neuroscience and evolution studies. The stability of the gut bacterial community of individual male and female zebra finches was assessed through repeat faecal sampling via culture and temperature gradient gel electrophoresis and partial sequencing of PCR-amplified eubacterial 16S rRNA gene products. Nineteen bacterial genera were detected across all samples (n = 99), with each bird carrying on average six operational taxonomic units. Using a novel statistical approach, we showed that bacterial assemblages and community richness varied between individual birds but remained stable over time within individuals. Neither the composition nor richness of bacterial communities differed significantly between the sexes. Our results show that zebra finches housed together under controlled conditions show consistent variation between individuals in their gut microflora that is not attributable to differences in host exposure to environmental microbial sources. Future studies could usefully explore the origin of this individual-specific variation and its consequences for host fitness and sexual selection.

Community dynamics in the mouse gut microbiota: a possible role for IRF9-regulated genes in community homeostasis

Background

Gut microbial communities of mammals are thought to show stable differences between individuals. This means that the properties imparted by the gut microbiota become a unique and constant characteristic of the host. Manipulation of the microbiota has been proposed as a useful tool in health care, but a greater understanding of mechanisms which lead to community stability is required. Here we have examined the impact of host immunoregulatory phenotype on community dynamics.

Methods and Findings

Denaturing gradient gel electrophoresis was used to analyse the faecal bacterial community of BALB/c and C57BL/6 mice and C57BL/6 mice deficient for either type I interferon (IFN) signalling (IRF9 KO mice) or type I and type II IFN signalling (STAT1 KO mice). Temporal variation was found in all mouse strains. A measure of the ability for a community structure characteristic of the host to be maintained over time, the individuality index, varied between mouse strains and available data from pigs and human models. IRF9 KO mice had significantly higher temporal variation, and lower individuality, than other mouse strains. Examination of the intestinal mucosa of the IRF9 KO mice revealed an increased presence of T-cells and neutrophils in the absence of inflammation.

Significance

The high temporal variation observed in the gut microbiota of inbred laboratory mice has implications for their use as experimental models for the human gut microbiota. The distinct IRF9 and STAT1 phenotypes suggest a role for IRF9 in immune regulation within the gut mucosa and that further study of interferon responsive genes is necessary to understand host-gut microbe relationships.

Site and strain-specific variation in gut microbiota profiles and metabolism in experimental mice

Background

The gastrointestinal tract microbiota (GTM) of mammals is a complex microbial consortium, the composition and activities of which influences mucosal development, immunity, nutrition and drug metabolism. It remains unclear whether the composition of the dominant GTM is conserved within animals of the same strain and whether stable GTMs are selected for by host-specific factors or dictated by environmental variables.

Methodology/Principal Findings

The GTM composition of six highly inbred, genetically distinct strains of mouse (C3H, C57, GFEC, CD1, CBA nu/nu and SCID) was profiled using eubacterial –specific PCR-DGGE and quantitative PCR of feces. Animals exhibited strain-specific fecal eubacterial profiles that were highly stable (c. >95% concordance over 26 months for C57). Analyses of mice that had been relocated before and after maturity indicated marked, reproducible changes in fecal consortia and that occurred only in young animals. Implantation of a female BDF1 mouse with genetically distinct (C57 and Agoutie) embryos produced highly similar GTM profiles (c. 95% concordance) between mother and offspring, regardless of offspring strain, which was also reflected in urinary metabolite profiles. Marked institution-specific GTM profiles were apparent in C3H mice raised in two different research institutions.

Conclusion/Significance

Strain-specific data were suggestive of genetic determination of the composition and activities of intestinal symbiotic consortia. However, relocation studies and uterine implantation demonstrated the dominance of environmental influences on the GTM. This was manifested in large variations between isogenic adult mice reared in different research institutions.

Production of 4-ethylphenol from 4-hydroxycinnamic acid by Lactobacillus sp. isolated from a swine waste lagoon

AIMS

To determine the source material and the responsible micro-organisms of 4-ethylphenol production in swine lagoon sediment slurries.

METHODS AND RESULTS

Swine lagoon sediment was blended and incubated with tryptone-yeast extract broth containing 10 mmol l(-1) each of 4-hydroxycinnamic as well as other phenolics. 4-Ethylphenol was only produced from 4-hydroxycinnamic acid. Denaturing gradient gel electrophoresis analysis indicated that the microbial community was substantially altered from inclusion of 4-hydroxycinnamic acid. Serial dilutions and selective plating were employed to isolate a culture capable of 4-hydroxycinnamic acid conversion to 4-ethylphenol. Morphological and ribosomal gene analysis indicated the isolate to be a Lactobacillus sp., Lactobacillus sp. pep8 converted 4-vinylphenol, but not 4-hydroxy-3-phenylpropionate, to 4-ethylphenol and did not convert 4-hydroxy-3-methoxycinnamic acid to 4-ethyl-2-methoxyphenol. A p-coumaric acid decarboxylase (pdc) gene identical to Lact. plantarum pdc genes was cloned from Lactobacillus sp. pep8.

CONCLUSIONS

Swine lagoon sediments produce 4-ethylphenol from 4-hydroxycinnamic acid due, in part, to the activity of Lactobacillus spp.

SIGNIFICANCE AND IMPACT OF THE STUDY

4-Ethylphenol, a malodourant of swine and beef wastes, is generated from plant materials by indigenous lactobacilli suggesting that altering the amount dietary of plant material may influence levels of 4-ethylphenol in the wastes.

Dietary protein and cellulose effects on chemical and microbial characteristics of Swine feces and stored manure

The objectives of this study were to investigate the effects of dietary crude protein (14.5 or 12.0%) and cellulose (8.7 or 2.5%) levels on composition of feces and manure after 8 wk of diet feeding and storage. Pigs were fed twice daily; after each feeding, urine and feces were collected and added to manure storage containers. On weeks 2 and 8 after initiation of the experiment, fresh fecal and manure samples were obtained. On Week 8, increased dietary cellulose resulted in significantly higher levels of volatile fatty acids (VFA) and phenols in feces compare to other diets. In contrast, dietary protein had the greatest effect on manure chemical composition; lower protein decreased sulfur content, ammonia, and phenolic compound concentrations. High levels of either dietary cellulose or protein tended to increase microbial community similarity in fecal samples, but only high protein increased similarity among manure sample microbial communities. Fecal and manure samples from Week 8 differed from samples taken in Week 2 both in chemical and microbiological composition. Week 2 samples had lower concentrations of many of chemical compounds and microbial diversity than samples from Week 8. The fecal results indicate that after 2 wk of feeding experimental diets the animals were not fully adapted to the diets. More importantly, after only 2 wk of urine and fecal collection, manure was not representative of stored manure, limiting its usefulness in developing standards and recommendations for on-farm management practices.

Probiotic therapy to men with incipient arteriosclerosis initiates increased bacterial diversity in colon: a randomized controlled trial

OBJECTIVE

This study aimed to clarify the microbial change in the intestinal microbiota in patients, with cardiovascular disease, consuming a drink with high numbers of live Lactobacillus plantarum.

METHODS

Sixteen males, with atherosclerotic plaque on the carotid wall, were randomly selected from a larger cohort and included in this double blind, placebo controlled study. Colonic biopsies, taken before and after four weeks of probiotic treatment, were analysed with Terminal Restriction Fragment Length Polymorphism, including digestion with MspI and HaeIII. Microbial diversity was calculated, short-chain fatty acids in faeces, and blood markers were analysed.

RESULTS

Consumption of one probiotic strain of L. plantarum (DSM 9843) increased intestinal microbial diversity. The probiotic group had an increased diversity after consumption of the probiotic drink compared to the change in the placebo group when Shannon and Weaner diversity index (MspI and HaeIII, p=0.026) and Simpson index of diversity (MspI, p=0.044 and HaeIII, p=0.026) were calculated. The fermentation pattern of short-chain fatty acids in faeces were unaffected for most acids, but the probiotic group had decreased concentration of isovaleric acid (p=0.006) and valeric acid (p=0.029). Viable count of lactobacilli increased in the probiotic group (p=0.001), but no significant changes in blood markers were observed.

CONCLUSION

Administration of a single-strain probiotic increases the bacterial diversity in the gut, and affects the concentration of some short-chain fatty acids. Consumption of the single strain L. plantarum DSM 9843 might be a strategy to favour a diverse intestinal microbiota, which is beneficial for the host.

Intestinal microflora molecular markers of spleen-deficient rats and evaluation of traditional Chinese drugs

AIM: To find a rapid and efficient analysis method of gastrointestinal microflora in Pi-deficient (spleen-deficient) rats and to evaluate traditional Chinese drugs.

METHODS: Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) based assay was performed to examine changes of intestinal microflora in two Pi-deficienct animal models and to evaluate the efficacy of four traditional Chinese drugs as well as a probiotic recipe and another therapy in Pi-deficient rats.

RESULTS: A molecular marker was identified for Pi-deficiency in rats. The pharmacodynamic evaluation system, including identified molecular markers (net integral area and abundance of DNA bands), Shannon’s index for diversity of intestinal microflora, and Sorenson’s pairwise similarity coefficient, was established. The four major clinical recipes of traditional Chinese drugs for Pi-deficiency in rats, especially at their medium dose (equivalence to the clinical dose), produced more pronounced recovery activities in Pi-deficient rats, while higher doses of these recipes did not show a better therapeutic effect but some toxic effects such as perturbation deterioration of intestinal microflora.

CONCLUSION: Both fingerprint analysis and identified marker can show Pi-deficiency in rats and its difference after treatment. The identified molecular marker may be applied in screening for the active compounds both in relative traditional Chinese drugs and in pharmacodynamic study of Pi-deficiency in rats.

Effects of calcium cyanamide on soil microbial communities and Fusarium oxysporum f. sp. cucumberinum

Calcium cyanamide (CaCN(2)) has been one of the potential candidates as soil disinfectant since the restriction of methyl bromide in soil fumigation due to its ecological risk. However, little information is available on effects of CaCN(2) on soil microbial community. In this study, the soil microbial communities and the fate of pathogen Fusarium oxysporum (Schlechtend, Fr) f. sp. cucumberinum (Owen) Snyder and Hansen (F.O. f. sp. cucumberinum) in response to CaCN(2) treatment was evaluated. F.O. f. sp. cucumberinum population in soil treated with CaCN(2) at rates of 80 and 200 gm(-2) was suppressed by 88.7 and 92.2% after 15 d of CaCN(2) application. Bacterial, fungal, and actinomycete populations were also greatly decreased after 3 d of CaCN(2) application, but they recovered to the control level by 15 d. The variation in functional diversity of soil microbes characterized by principal component analysis, diversity and evenness indices based on Biolog data followed a similar trend. Meanwhile, the band number from the DGGE of soil 16S rDNA fragments increased from 9 for the non-CaCN(2)-treated soil to 10 or 12 after different rates of CaCN(2) application at 15 d, indicating the increase of abundant rDNA types in the community. The results suggest that CaCN(2) application had only a short-term and transitory impact on the indigenous soil microbial community in contrast to the long-term suppression of the F.O. f. sp. cucumberinum population. It is feasible to reduce Fusarium wilt without significant impact on microbial community by application of CaCN(2) at reasonable doses.

Molecular analysis of microbiota along the digestive tract of juvenile Atlantic salmon (Salmo salar L.)

Dominant bacterial microbiota of the gut of juvenile farmed Atlantic salmon was investigated using a combination of molecular approaches. Bacterial community composition from the stomach, the pyloric caeca, and the intestine was assessed by extracting DNA directly from each gut compartment. Temporal temperature gradient gel electrophoresis (TTGE) analysis of 16S ribosomal DNA (rDNA) amplicons showed very similar bacterial compositions throughout the digestive tract. Band sequencing revealed a narrow diversity of species with a dominance of Pseudomonas in the three compartments. However, cloning revealed more diversity among the Pseudomonas sequences. To confirm these results, we analyzed the bacterial community by amplifying the variable 16S-23S rDNA intergenic spacer region (ITS). Similar ITS profiles were observed among gastrointestinal compartments of salmon, confirming the TTGE results. Moreover, the dominant ITS band at 650 bp, identified as Pseudomonas, was observed in the ITS profile from fish collected in two seasons (July 2003 and 2004). In contrast, aerobic culture analysis revealed Shewanella spp. as the most prevalent isolate. This discrepancy was resolved by evaluating 16S rDNA and ITS polymerase chain reaction amplification efficiency from both Shewanella and Pseudomonas isolates. Very similar efficiencies were observed in the two bacteria. Hence, this discrepancy may be explained by preferential cultivation of Shewanella spp. under the experimental conditions. Also, we included analyses of pelleted feed and the water influent to explore environmental influences on the bacterial composition of the gut microbiota. Overall, these results indicate a homogeneous composition of the bacterial community composition along the gastrointestinal tract of reared juvenile salmon. This community is mainly composed of Pseudomonas spp., which could be derived from water influent and may be selectively associated with salmon in this hatchery.

Technical note: Bacterial diversity and fermentation end products in rumen fluid samples collected via oral lavage or rumen cannula

A study was conducted to determine if sampling rumen contents via a ruminal cannula or oral lavage tube would yield similar denaturing gradient gel electrophoresis profiles of the bacterial community. Two species of ruminally cannulated animals were used for this study (cattle, n = 2; sheep, n = 3). All animals were allowed ad libitum access to feed. Cattle were fed baled unprocessed sorghum-sudan hay (12% CP, 68% NDF; DM basis), whereas sheep were maintained on chopped alfalfa (18% CP, 40% NDF; DM basis). Ruminal fluid was collected (approximately 20 mL) once per week for 3 wk from each animal using a poly tube equipped with a suction strainer with a hand-held suction pump through the rumen cannula or oral cavity. The denaturing gradient gel electrophoresis analysis demonstrates that yield of bacterial diversity was not different between the 2 sampling methods (P = 0.73). When samples were grouped according to band pattern similarity, groups were most stable according to individual animal and species rather than sampling method. Total VFA and molar proportions of individual VFA did not differ by sampling method (P > 0.40). Additionally, rumen ammonia concentrations were similar for both sampling methods (19.3 vs. 19.1 mM +/- 8.0 for cannula vs. lavage, respectively; P = 0.98). These data indicate that rumen samples collected via oral lavage or rumen cannula yield similar results. This knowledge will allow sample collection from a greater population of animals and an ability to maintain the value of research livestock that can be lost due to the surgical implantation of a ruminal cannula.

Gender difference in the composition of fecal flora in laboratory mice, as detected by denaturing gradient gel electrophoresis (DGGE)

The difference between genders in the composition of mouse fecal flora was examined. A polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were performed on the V6-V8 regions of bacterial 16S rDNA obtained from fecal samples at 0, 1, 2, 3, 4, and 8 weeks after the introduction of mice into the laboratory from a mouse farm. Cluster analysis and non-metric multidimensional scaling (NMDS) were then performed. Male and female mice were distributed on opposite sides of the origin of the plane in NMDS at weeks 0, 2, 3, and 8. These results suggest a gender difference in the composition of intestinal flora in mice.

Microbial ecology shifts in the ileum of broilers during feed withdrawal and dietary manipulations

Broilers are withheld from feed for 8 to 24 h before processing to empty the gastrointestinal tract and reduce potential carcass contamination from gastrointestinal tract contents. Intestinal microbial changes during feed withdrawal (FW) have not been thoroughly defined. Two experiments were conducted to examine the effects of diet and FW on the microbial ecology in the small intestine. In experiment 1, 42-d-old broilers were fed diets containing no additive (control), 250 ppm of CuSO(4), or bacitracin (BMD; 30 ppm) and were also subjected to FW for 0, 10, and 24 h. Six birds from each dietary treatment were killed at each FW time point and ileal mucosa and digesta were collected. Microbial communities were determined by isolating bacterial DNA, amplifying the V3 region of 16S ribosomal DNA, and performing denaturing gradient gel electrophoresis. The mucosal microbial profiles from birds at 0 h of FW had higher similarity values than those at 24 h of FW, indicating that as FW time increased, uniformity of intestinal microbial populations decreased. Numbers of bands (an indicator of numbers of bacterial species present) at 0 h (9.38) were greater than those at 10 and 24 h (5.39 and 5.78, respectively), suggesting a reduction in microbial species and diversity as FW time increased. Copper-fed birds had greater similarity coefficients than either the control or BMD-fed birds, but BMD-fed birds had greater band numbers. No interaction between diet and FW was observed and no digesta differences were observed. In experiment 2, 62-d-old birds fed corn-soy diets in floor pens were subjected to 0, 8, 12, and 24 h of FW. Ileal mucosal tissue was collected and analyzed as in experiment 1. Mucosal microbiota similarities were greater at 0 h of FW than at 8, 12, or 24 h of FW and band numbers were reduced between 0 and 24 h of FW. Data from these studies suggest that FW and dietary treatments alter the microbial community of the intestine by decreasing bacterial diversity in the ileum.

Change in the ileal bacterial population of turkeys fed different diets and after infection with Salmonella as determined with denaturing gradient gel electrophoresis of amplified 16s ribosomal DNA

Changes in ileal bacterial populations of Salmonella-infected turkeys fed different diets were analyzed by using 16S-V3 PCR denaturing gradient gel electrophoresis. Turkeys raised on litter flooring were fed wheat- and corn-based diets with and without enzyme preparations (XY1 and XY2, respectively) from 0 to 126 d. Preparation XY1 contained exclusively endoxylanase, whereas preparation XY2 contained endoxylanase, protease, and alpha-amylase (Danisco, , Wiltshire, UK). The dietary activity levels of XY1 and XY2 were 2,500 and 650 endo-1,4-beta-xylanase units/kg of feed, respectively. Microbial DNA was extracted from the ileal content of 16-wk-old turkeys, and the 16S rDNA gene was amplified by PCR and analyzed by denaturing gradient gel electrophoresis. Diversity indexes, including richness (number of species, S), evenness (relative distribution of species, EH), diversity (using Shannon's index, H'), and Sorenson's pairwise similarities coefficient (measures the species in common between different habitats, Cs) were calculated. Additionally, diversity indexes were associated with Salmonella prevalence determined from fresh fecal droppings collected from each pen. On the basis of contrast analysis, the wheat-based diets resulted in higher microbial diversity indexes than the corn-based diets (S = 10 vs. 12; EH = 0.9 vs. 0.8; H' = 2.2 vs. 1.9, P < 0.05). Likewise, enzyme supplementation stimulated growth of the microbiota and increased the diversity indexes in comparison with unsupplemented treatments (S = 13 vs. 10; EH = 0.9 vs. 0.8; H' = 2.2 vs. 1.9, P < 0.05). Salmonella prevalence was higher (P < 0.05) at 15 wk in turkeys fed the corn-based diet (Salmonella prevalence = 50%) than in turkeys fed the corn-enzyme (Salmonella prevalence = 13%) and wheat-based (Salmonella prevalence = 0%) dietary treatments. Therefore, contrast analysis showed that birds fed the corn control diet had lower microbiota diversity but higher Salmonella prevalence than birds fed the enzyme-supplemented and wheat-based diets. In contrast, birds fed the wheat-based diets had higher diversity but lower Salmonella prevalence than birds fed the corn-based diets. High dietary nonstarch polysaccharides from wheat and dietary exogenous enzyme supplementation promoted microbial community diversity and apparently discouraged Salmonella colonization through competitive exclusion. Nonstarch polysaccharides and dietary exogenous enzyme supplementation may be practical tools to control enteric pathogens and benefit the intestinal health and food safety of the birds.

The effect of gender on the bacterial community in the gastrointestinal tract of broilers

The effect of gender on the growth, carcass yield, and nutritional requirements of chickens has been well documented, but little is known about how the sex of a chicken affects the bacterial population of the gastrointestinal tract. Therefore, our objective was to evaluate the biodiversity of the bacterial community in the gastrointestinal tract of male and female broilers. An experiment was conducted with Cobb 500 broiler chicks that were vent sexed at 0 d of age and allocated to 8 pens of 25 chicks per gender. All birds were fed a nonmedicated corn-soybean meal starter diet from 0 to 21 d of age. At 3, 7, 14, and 21 d of age, chicks were randomly selected and ileums were taken for bacterial sampling. Bacterial DNA was isolated from the digesta of the ileum, and denaturing gradient gel electrophoresis was used to examine PCR-amplified fragments of 16S ribosomal DNA. Denaturing gradient gel electrophoresis analyses revealed that the bacterial communities separated into 2 gender-specific groups, with less than 30% similarity between populations. Furthermore, as the birds aged, the similarity of the intestinal bacterial community decreased within each gender. Although ileal bacterial population differences within and between genders were noted as early as d 3, differences in growth rate between males and females were not noted until d 21 (data not shown). This suggested that non-growth-related factors influenced the composition of intestinal bacterial communities.

Inhomogeneity of fecal flora in separately reared laboratory mice, as detected by denaturing gradient gel electrophoresis (DGGE)

Laboratory mice were divided into 2 groups and introduced to different rooms immediately after being transferred from a mouse farm. Polymerase chain reaction followed by denaturing gradient gel electrophoresis were performed on the V6-V8 regions of bacterial 16S rDNA obtained from fecal samples at 0, 1, 2, 3, 4 and 8 weeks after the introduction. Binary data were obtained from banding patterns, and Euclidean distances for each week were calculated and analyzed by cluster analysis and non-metric multidimensional scaling. Euclidean distances were significantly higher at weeks 1 and 2 than at week 0 in both groups, although the distances between the 2 groups were significantly higher after week 1 than week 0. The distances between the 2 groups were significantly higher than those within each group at weeks 4 and 8. Mice in the 2 groups formed clusters at weeks 2 and 3 respectively, and mice were divided into 2 clusters by their respective groups at weeks 4 and 8. Mice in the 2 groups were distributed on opposite sides of the origin on the 2-dimensional plane after week 2. These results suggest that mouse fecal flora changed characteristically, according to the local environment after introduction.

Identification of bacteria from blood in febrile patients with ulcerative colitis by terminal restriction fragment length polymorphism profile analysis of 16S rRNA gene

OBJECTIVE

Recently, highly sensitive molecular-biological approaches using the 16S rRNA gene sequence have been carried out for the detection of bacteria. The aim of this study was to detect bacteremia in febrile patients with ulcerative colitis (UC) using a new molecular approach.

MATERIAL AND METHODS

Fifteen febrile patients with relapsing UC were enrolled, and 15 healthy volunteers participated as normal controls. Blood samples were analyzed for bacteremia using nested polymerase chain reaction (PCR) with universal primers (27F, 529F, 1492R). We investigated the bacterial DNA by means of terminal restriction fragment length polymorphism (T-RFLP) with five restriction enzymes (Alu I, Hha I, Hae III, Msp I, and Rsa I). A terminal restriction fragment (TRF) profile database was created with the predicted profiles of 63 common bacteria isolated from blood cultures, using computer simulation based on sequence information. TRF lengths were analyzed using the TRF profile database and a T-RFLP profiler.

RESULTS

The bacterial gene was detected in 9 out of 15 UC patients (60%) and 8 of out 15 controls (53%). The numbers of Hae III- and Rsa I-digested T-RFs and the average number of five restriction enzyme-digested T-RFs were significantly higher in UC patients than in controls (p=0.0189, 0.0151, 0.0092, respectively). In UC patients, the most prevalent species included the 7 common species in controls and 10 other species.

CONCLUSIONS

In febrile UC patients with relapse, bacteremia undetected by culture was found at high frequency by the PCR method. Therefore, antibiotic treatment for UC can be approved on the basis of the finding of bacteremia in this study.

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.