Diversity and succession of the intestinal bacterial community of the maturing broiler chicken

The diversity of bacterial floras in the ilea and ceca of chickens that were fed a vegetarian corn-soy broiler diet devoid of feed additives was examined by analysis of 1,230 partial 16S rRNA gene sequences. Nearly 70% of sequences from the ileum were related to those of Lactobacillus, with the majority of the rest being related to Clostridiaceae (11%), Streptococcus (6.5%), and Enterococcus (6.5%). In contrast, Clostridiaceae-related sequences (65%) were the most abundant group detected in the cecum, with the other most abundant sequences being related to Fusobacterium (14%), Lactobacillus (8%), and Bacteroides (5%). Statistical analysis comparing the compositions of the different 16S rRNA libraries revealed that population succession occurred during some sampling periods. The significant differences among cecal libraries at 3 and 7 days of age, at 14 to 28 days of age, and at 49 days of age indicated that successions occurred from a transient community to one of increasing complexity as the birds aged. Similarly, the ileum had a stable bacterial community structure for birds at 7 to 21 days of age and between 21 to 28 days of age, but there was a very unique community structure at 3 and 49 days of age. It was also revealed that the composition of the ileal and cecal libraries did not significantly differ when the birds were 3 days old, and in fact during the first 14 days of age, the cecal microflora was a subset of the ileal microflora. After this time, the ileum and cecum had significantly different library compositions, suggesting that each region developed its own unique bacterial community as the bird matured.     

Effect of dietary supplementation with a Saccharomyces cerevisiae mannan oligosaccharide on the bacterial community structure of broiler cecal contents

This study investigated the effects of dietary supplementation with a prebiotic mannan oligosaccharide (MOS) on broiler performance, bacterial community structure, and phylogenetic populations of cecal contents. Bird performance data were collected, and cecal samples were extracted from randomly caught poults from each treatment group every 7 days from hatching to the age of 42 days. Weight gain, feed consumption, and feed efficiency ratios did not differ significantly between groups. Automated ribosomal intergenic spacer analysis (ARISA) of the bacterial communities in birds receiving MOS-supplemented diets indicated that dietary supplementation with MOS at either of 2 levels significantly altered the bacterial community structure from that of the control group on all sample days. The phylogenetic identities of bacteria contained within the cecum were determined by constructing a 16S rRNA gene clone library. A total of 594 partial 16S rRNA gene sequences from the cecal contents were analyzed and compared for the three dietary treatments. The dominant bacteria of the cecum belonged to three phyla, Firmicutes, Bacteroidetes, and Proteobacteria; of these, Firmicutes were the most dominant in all treatment groups. Statistical analysis of the bacterial 16S rRNA gene clone libraries showed that the compositions of the clone libraries from broilers receiving MOS-supplemented diets were, in most cases, significantly different from that of the control group. It can be concluded that in this trial MOS supplementation significantly altered the cecal bacterial community structure.     

Bacteria and Methanogens Differ along the Gastrointestinal Tract of Chinese Roe Deer (Capreolus pygargus)

The current study provides the insight into the bacteria in the gastrointestinal tract (GIT) and methanogens presented in the rumen and cecum of the Chinese roe deer (Capreolus pygargus). The ruminal, ileal, cecal, and colonic contents, as well as feces, were obtained from each of the three, free-range, roe deer ingesting natural pasture after euthanasia. For the bacterial community, a total of 697,031 high-quality 16S rRNA gene sequences were generated using high-throughput sequencing, and assigned to 2,223 core operational taxonomic units (OTUs) (12 bacterial phyla and 87 genera). The phyla Firmicutes (51.2%) and Bacteroidetes (39.4%) were the dominant bacteria in the GIT of roe deer. However, the bacterial community in the rumen was significantly (P<0.01) different from the other sampled regions along the GIT. Secondly, Prevotella spp., Anaerovibrio spp., and unidentified bacteria within the families Veillonellaceae and Paraprevotellaceae were more abundant in the rumen than in the other regions. Unidentified bacteria within the family Enterobacteriaceae, Succinivibrio spp., and Desulfovibrio spp. were more predominant in the colon than in other regions. Unidentified bacteria within the family Ruminococcaceae, and Bacteroides spp. were more prevalent in the ileum, cecum and fecal pellets. For methanogens in the rumen and cecum, a total of 375,647 high quality 16S rRNA gene sequences were obtained and assigned to 113 core OTUs. Methanobrevibacter millerae was the dominant species accounting for 77.3±7.4 (S.E) % and 68.9±4.4 (S.E) % of total sequences in the rumen and cecum of roe deer, respectively. However, the abundance of Methanobrevibacter smithii was higher in the rumen than in the cecum (P = 0.004). These results revealed that there was intra variation in the bacterial community composition across the GIT of roe deer, and also showed that the methanogen community in the rumen differed from that in the cecum.     

Effects of adherent Lactobacillus cultures on growth,weight of organs and intestinal microflora and volatile fatty acids in broilers

A total of 180 1-day old Arbor Acres chicks was used to investigate the effects of a single L. acidophilus I 26 strain or a mixture of 12 Lactobacillus cultures on the production performance, weight of organs, and intestinal microflora and VFA of broilers. The chicks were assigned randomly into three groups with 60 chicks per treatment. The three dietary treatments were: (i) basal diet (acted as control); (ii) basal diet+1 g kg⁻¹ L. acidophilus I 26; and (iii) basal diet+1 g kg⁻¹ mixture of 12 Lactobacillus strains. The results showed that the addition of either a single L. acidophilus I 26 strain or a mixture of 12 Lactobacillus cultures to the basal diet increased significantly (P<0.05) the body weight and feed:gain ratio of broilers for 0–6 weeks. Supplementing the Lactobacillus cultures, singly or in a mixture, in the diet of broilers also decreased significantly (P<0.05) the numbers of coliforms in the cecum 10 and 20 days after feeding, increased significantly (P<0.05) the total VFA in the ileum and cecum, and lowered the cecal pH values. However, the addition of the Lactobacillus cultures in the diets did not increase significantly the lactobacilli population in the ileum and cecum of broilers, except for 30 days after feeding. There were also no significant differences in the populations of total anaerobes, total aerobes, Bifidobacteria and Streptococcus in the ileal and cecal contents of chickens fed with or without Lactobacillus cultures. No significant differences were found in the weight of the liver, spleen, bursa, gizzard, duodenum, jeju-ileum and total small intestine of broilers given the different dietary treatments.     

Characterization of Intestinal Microbiota and Response to Dietary Virginiamycin Supplementation in the Broiler Chicken

The inclusion of antibiotic growth promoters, such as virginiamycin, at subtherapeutic levels in poultry feeds has a positive effect on health and growth characteristics, possibly due to beneficial effects on the host gastrointestinal microbiota. To improve our understanding of the chicken gastrointestinal microbiota and the effect of virginiamycin on its composition, we characterized the bacteria found in five different gastrointestinal tract locations (duodenal loop, mid-jejunum, proximal ileum, ileocecal junction, and cecum) in 47-day-old chickens that were fed diets excluding or including virginiamycin throughout the production cycle. Ten libraries (five gastrointestinal tract locations from two groups of birds) of approximately 555-bp chaperonin 60 PCR products were prepared, and 10,932 cloned sequences were analyzed. A total of 370 distinct cpn60 sequences were identified, which ranged in frequency of recovery from 1 to 2,872. The small intestinal libraries were dominated by sequences from the Lactobacillales (90% of sequences), while the cecum libraries were more diverse and included members of the Clostridiales (68%), Lactobacillales (25%), and Bacteroidetes (6%). To assess the effects of virginiamycin on the gastrointestinal microbiota, 15 bacterial targets were enumerated using quantitative, real-time PCR. Virginiamycin was associated with increased abundance of many of the targets in the proximal gastrointestinal tract (duodenal loop to proximal ileum), with fewer targets affected in the distal regions (ileocecal junction and cecum). These findings provide improved profiling of the composition of the chicken intestinal microbiota and indicate that microbial responses to virginiamycin are most significant in the proximal small intestine.     

Adaptation of the Cecal Bacterial Microbiome of Growing Pigs in Response to Resistant Starch Type 4

Resistant starch (RS) exacerbates health benefits on the host via modulation of the gut bacterial community. By far, these effects have been less well explored for RS of type 4. This study aimed at gaining a community-wide insight into the impact of enzymatically modified starch (EMS) on the cecal microbiota and hindgut fermentation in growing pigs. Castrated male pigs (n = 12/diet; 29-kg body weight) were fed diets with either 70% EMS or control starch for 10 days. The bacterial profile of each cecal sample was determined by sequencing of the V345 region of the 16S rRNA gene using the Illumina MiSeq platform. EMS diet reduced short-chain fatty acid concentrations in cecum and proximal colon compared to the control diet. Linear discriminant analyses and K means clustering indicated diet-specific cecal community profiles, whereby diversity and species richness were not different among diets. Pigs showed host-specific variation in their most abundant phyla, Firmicutes (55%), Proteobacteria (35%), and Bacteroidetes (10%). The EMS diet decreased abundance of Ruminococcus, Parasutterella, Bilophila, Enterococcus, and Lactobacillus operational taxonomic units (OTU), whereas Meniscus and Actinobacillus OTU were increased compared to those with the control diet (P < 0.05). Quantitative PCR confirmed results for host effect on Enterobacteriaceae and diet effect on members of the Lactobacillus group. The presence of less cecal short-chain fatty acids and the imputed metabolic functions of the cecal microbiome suggested that EMS was less degradable for cecal bacteria than the control starch. The present EMS effects on the bacterial community profiles were different than the previously reported RS effects and can be linked to the chemical structure of EMS.     

Growth performance,intestinal histomorphology,gut microflora and ghrelin gene expression analysis of broiler by supplementing natural growth promoters: A nutrigenomics approach

In an epoch of escalating number of antibiotic-resistance bacteria, there is a dire need to develop efficient and novel feeding strategies for animal nutrition as alternatives to antibiotics. Here, implicating nutrigenomic approach, phytobiotics and organic acids were used to evaluate ghrelin gene expression levels, gut microflora composition, performance parameters and intestinal histomorphological changes in broiler chickens. One-day-old chicks (n = 315) were reared for 42 days and distributed randomly into five experimental groups; each with three replicates (21 birds per replicate). Experimental groups were control: basal diet only, antimicrobial growth promoter: 40 g/metric ton of basal diet (virginiamycin), organic acids: 4 kg/metric ton of basal diet, phytobiotics: 3 kg/metric ton of basal diet, combination: 7 kg/metric ton of basal diet (organic acids 4 kg and phytobiotics 3 kg metric ton of feed). Growth performance, histological and ghrelin gene expression analysis were executed on 21 and 42 days while, quantitative bacterial analysis of cecum and ileum was performed on day 42. Increased feed intake and body weight (p < 0.05) were noticed in phytobiotics group. Addition of phytobiotics significantly improved (p < 0.05) villus height and ratio of villus height/crypt depth in ileum, jejunum, and duodenum and down-regulated ghrelin gene expression levels. Total coliform and Escherichia coli in cecal and ileal digesta were decreased significantly (p < 0.05) in organic acids group. Correlation analysis revealed Lactobacillus spp. were positively correlated to villus height/crypt depth ration in duodenum. The findings indicated the importance of gene-nutrient-microbiota interactions based on nutrigenomics approach. Hence, phytobiotics and organic acids might be suitable alternatives to antibiotics for improved performance and immunity, along with healthier meat production in poultry.     

Molecular Diversity of Lactobacillus spp. and Other Lactic Acid Bacteria in the Human Intestine as Determined by Specific Amplification of 16S Ribosomal DNA

A Lactobacillus group-specific PCR primer, S-G-Lab-0677-a-A-17, was developed to selectively amplify 16S ribosomal DNA (rDNA) from lactobacilli and related lactic acid bacteria, including members of the genera Leuconostoc, Pediococcus, and Weissella. Amplicons generated by PCR from a variety of gastrointestinal (GI) tract samples, including those originating from feces and cecum, resulted predominantly in Lactobacillus-like sequences, of which ca. 28% were most similar to the 16S rDNA of Lactobacillus ruminis. Moreover, four sequences of Leuconostoc species were retrieved that, so far, have only been detected in environments other than the GI tract, such as fermented food products. The validity of the primer was further demonstrated by using Lactobacillus-specific PCR and denaturing gradient gel electrophoresis (DGGE) of the 16S rDNA amplicons of fecal and cecal origin from different age groups. The stability of the GI-tract bacterial community in different age groups over various time periods was studied. The Lactobacillus community in three adults over a 2-year period showed variation in composition and stability depending on the individual, while successional change of the Lactobacillus community was observed during the first 5 months of an infant’s life. Furthermore, the specific PCR and DGGE approach was tested to study the retention in fecal samples of a Lactobacillus strain administered during a clinical trial. In conclusion, the combination of specific PCR and DGGE analysis of 16S rDNA amplicons allows the diversity of important groups of bacteria that are present in low numbers in specific ecosystems to be characterized, such as the lactobacilli in the human GI tract.     

Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation

This study focused on identifying reproducible effects of dietary supplementation with a mannan oligosaccharide (MOS) on the broiler cecal bacterial community structure and function in a commercial production setting. Two separate trials, each with a control and a supplemented group, were carried out in the same commercial location and run concurrently. Approximately 10,000 birds from the same commercial hatchery were mirror imaged into each of four commercial broiler sheds and fed either a control or supplemented diet. Cecal contents were obtained on days 7, 21, and 35 posthatch from 12 randomly caught broilers from each group. Bacterial pyrosequencing was performed on all samples, with approximately 250,000 sequences obtained per treatment per time point. The predominant phyla identified at all three time points in both trials were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Tenericutes, representing >99% of all sequences. MOS supplementation altered the bacterial community composition from 7 days supplementation through 35 days supplementation. Bacteroidetes appeared to be replacing Firmicutes as a result of supplementation, with the most noticeable effects after 35 days. The effects of supplementation were reproducible across both trials. PICRUSt was used to identify differences between the functional potentials of the bacterial communities as a result of MOS supplementation. Using level 3 KEGG ortholog function predictions, differences between control and supplemented groups were observed, with very strong segregation noted on day 35 posthatch in both trials. This indicated that alterations of bacterial communities as a result of MOS are likely to alter the functional capability of the cecum.     

Bacteria,phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between small and large intestinal locations, including enrichment of Firmicutes and phage-encoding genes in the ileum. The large intestinal microbiota encoded numerous genes to degrade plant cell wall components, and these genes were lacking in the ileum. The mucosa-associated ileal microbiota harbored greater bacterial diversity than the lumen but similar membership to the mucosa of the large intestine, suggesting that most gut microbes can associate with the mucosa and might serve as an inoculum for the lumen. The collateral effects on the microbiota of antibiotic-fed animals caused divergence from that of control animals, with notable changes being increases in Escherichia coli populations in the ileum, Lachnobacterium spp. in all gut locations, and resistance genes to antibiotics not administered. Characterizing the differential metabolic capacities and response to perturbation at distinct intestinal locations will inform strategies to improve gut health and food safety.     

Quantitative Detection of Clostridium perfringens in the Broiler Fowl Gastrointestinal Tract by Real-Time PCR

Strains of Clostridium perfringens are a frequent cause of food-borne disease and gas gangrene and are also associated with necrotic enteritis in chickens. To detect and quantify the levels of C. perfringens in the chicken gastrointestinal tract, a quantitative real-time PCR assay utilizing a fluorogenic, hydrolysis-type probe was developed and utilized to assay material retrieved from the broiler chicken cecum and ileum. Primers and probe were selected following an alignment of 16S rDNA sequences from members of cluster I of the genus Clostridium, and proved to be specific for C. perfringens. The assay could detect approximately 50 fg of C. perfringens genomic DNA and approximately 20 cells in pure culture. Measurements of the analytical sensitivity determined with spiked intestinal contents indicated that the consistent limit of detection with ileal samples was approximately 10² CFU/g of ileal material, but only about 10⁴ CFU/g of cecal samples. The decreased sensitivity with the cecal samples was due to the presence of an unidentified chemical PCR inhibitor(s) in the cecal DNA purifications. The assay was utilized to rapidly detect and quantify C. perfringens levels in the gut tract of broiler chickens reared without supplementary growth-promoting antibiotics that manifested symptoms of necrotic enteritis. The results illustrated that quantitative real-time PCR correlates well with quantification via standard plate counts in samples taken from the ileal region of the gastrointestinal tract.     

16S rRNA-Based Analysis of Microbiota from the Cecum of Broiler Chickens

The microbiota of the intestinal tract of chickens plays an important role in inhibiting the establishment of intestinal pathogens. Earlier culturing and microscopic examinations indicated that only a fraction of the bacteria in the cecum of chickens could be grown in the laboratory. Therefore, a survey of cecal bacteria was done by retrieval of 16S rRNA gene sequences from DNA isolated from the cecal content and the cecal mucosa. The ribosomal gene sequences were amplified with universal primers and cloned or subjected to temporal temperature gradient gel electrophoresis (TTGE). Partial 16S rRNA gene sequences were determined from the clones and from the major bands in TTGE gels. A total of 1,656 partial 16S rRNA gene sequences were obtained and compared to sequences in the GenBank. The comparison indicated that 243 different sequences were present in the samples. Overall, sequences representing 50 phylogenetic groups or subgroups of bacteria were found, but approximately 89% of the sequences represented just four phylogenetic groups (Clostridium leptum, Sporomusa sp., Clostridium coccoides, and enterics). Sequences of members of the Bacteroides group, the Bifidobacterium infantis subgroup, and of Pseudomonas sp. each accounted for less than 2% of the total. Sequences related to those from the Escherichia sp. subgroup and from Lactobacillus, Pseudomonas, and Bifidobacterium spp. were generally between 98 and 100% identical to sequences already deposited in the GenBank. Sequences most closely related to those of the other bacteria were generally 97% or less identical to those in the databases and therefore might be from currently unknown species. TTGE and random cloning indicated that certain phylogenetic subgroups were common to all birds analyzed, but sequence data from random cloning also provided evidence for qualitative and quantitative differences among the cecal microbiota of individual birds reared under very similar conditions.     

Ecological succession of bacterial communities during conventionalization of germ-free mice

Little is known about the dynamics of early ecological succession during experimental conventionalization of the gastrointestinal (GI) tract; thus, we measured changes in bacterial communities over time, at two different mucosal sites (cecum and jejunum), with germfree C57BL/6 mice as the recipients of cecal contents (input community) from a C57BL/6 donor mouse. Bacterial communities were monitored using pyrosequencing of 16S rRNA gene amplicon libraries from the cecum and jejunum and analyzed by a variety of ecological metrics. Bacterial communities, at day 1 postconventionalization, in the cecum and jejunum had lower diversity and were distinct from the input community (dominated by either Escherichia or Bacteroides). However, by days 7 and 21, the recipient communities had become significantly diverse and the cecal communities resembled those of the donor and donor littermates, confirming that transfer of cecal contents results in reassembly of the community in the cecum 7 to 21 days later. However, bacterial communities in the recipient jejunum displayed significant structural heterogeneity compared to each other or the donor inoculum or the donor littermates, suggesting that the bacterial community of the jejunum is more dynamic during the first 21 days of conventionalization. This report demonstrates that (i) mature input communities do not simply reassemble at mucosal sites during conventionalization (they first transform into a "pioneering" community and over time take on the appearance, in membership and structure, of the original input community) and (ii) the specific mucosal environment plays a role in shaping the community.     

Effective Recovery of Bacterial DNA and Percent-Guanine-Plus-Cytosine-Based Analysis of Community Structure in the Gastrointestinal Tract of Broiler Chickens

A DNA-based, direct method for initial characterization of the total bacterial community in ileum and cecum of the chicken gastrointestinal (GI) tract was developed. The efficiencies of bacterial extraction and lysis were >95 and >99%, respectively, and therefore the DNA recovered should accurately reflect the bacterial communities of the ileal and cecal digesta. Total bacterial DNA samples were fractionated according to their percent G+C content. The profiles reflecting the composition of the bacterial community were reproducible within each compartment, but different between the compartments of the GI tract. This approach is independent of the culturability of the bacteria in the consortium and can be used to improve our understanding of how diet and other variables modulate the microbial communities of the GI tracts of animals.     

Culture-Independent Analysis of Gut Bacteria: the Pig Gastrointestinal Tract Microbiota Revisited

The phylogenetic diversity of the intestinal bacterial community in pigs was studied by comparative 16S ribosomal DNA (rDNA) sequence analysis. Samples were collected from a total of 24 pigs representing a variety of diets, ages, and herd health status. A library comprising 4,270 cloned 16S rDNA sequences obtained directly by PCR from 52 samples of either the ileum, the cecum, or the colon was constructed. In total, 375 phylotypes were identified using a 97% similarity criterion. Three hundred nine of the phylotypes (83%) had a <97% sequence similarity to any sequences in the database and may represent yet-uncharacterized bacterial genera or species. The phylotypes were affiliated with 13 major phylogenetic lineages. Three hundred four phylotypes (81%) belonged to the low-G+C gram-positive division, and 42 phylotypes (11.2%) were affiliated with the Bacteroides and Prevotella group. Four clusters of phylotypes branching off deeply within the low-G+C gram-positive bacteria and one in the Mycoplasma without any cultured representatives were found. The coverage of all the samples was 97.2%. The relative abundance of the clones approximated a lognormal distribution; however, the phylotypes detected and their abundance varied between two libraries from the same sample. The results document that the intestinal microbial community is very complex and that the majority of the bacterial species colonizing the gastrointestinal tract in pigs have not been characterized.     

金针菇菇脚对肉鸡肠道菌群的影响

目的研究金针菇菇脚(Flammulina velutipes stembase,FVS)对肉鸡生长性能、肠道发育及肠道菌群的影响。方法选取4 550只1日龄爱拔益加(AA)肉鸡,随机分为5组:空白组(基础日粮)、2%FVS组(基础日粮+2%FVS)、4%FVS组(基础日粮+4%FVS)、6%FVS组(基础日粮+6%FVS)和6%FVS阶段组(基础日粮+试验第1、3、5周饲喂含有6%FVS的日粮,于试验2、4、6周饲喂基础日粮)。试验为期42d。结果 FVS组肉鸡平均日增重量均显著高于空白组(P0.05)。6%FVS组和6%FVS阶段组肉鸡平均日采食量显著高于空白组(P0.05)。FVS组肉鸡料重比均显著低于空白组(P0.05)。与空白组相比,日龄21d时,2%FVS组肉鸡回肠和盲肠重量均显著增加(P0.05);4%FVS组十二指肠长度和盲肠重量均显著增加(P0.05);6%FVS阶段组十二指肠长度及重量、空肠长度及重量和回肠重量均显著增加(P0.05)。与空白组相比,日龄42d时,2%FVS组肉鸡十二指肠长度和重量及盲肠重量均显著增加(P0.05);4%FVS组十二指肠长度和重量、回肠长度和盲肠长度及重量均显著增加(P0.05);6%FVS组十二指肠长度和盲肠长度及重量均显著增加(P0.05);6%FVS阶段组十二指肠重量、空肠重量和回肠长度及重量均显著增加(P0.05)。与空白组相比,日龄21d时6%FVS阶段组肉鸡盲肠菌群DNA条带数显著增加;日龄42d时FVS组肉鸡盲肠菌群DNA条带数均显著增加。日龄21d和42d时肉鸡盲肠菌群共性条带中均含有扭链胃球菌(Ruminococcus torques),而FVS组含有大量的产酸菌。结论日粮中添加FVS可提高肉鸡生长能力、促进肠道发育、增加肠道菌群多样性。     

Identification of a Core Bacterial Community within the Large Intestine of the Horse

The horse has a rich and complex microbial community within its gastrointestinal tract that plays a central role in both health and disease. The horse receives much of its dietary energy through microbial hydrolysis and fermentation of fiber predominantly in the large intestine/hindgut. The presence of a possible core bacterial community in the equine large intestine was investigated in this study. Samples were taken from the terminal ileum and 7 regions of the large intestine from ten animals, DNA extracted and the V1-V2 regions of 16SrDNA 454-pyrosequenced. A specific group of OTUs clustered in all ileal samples and a distinct and different signature existed for the proximal regions of the large intestine and the distal regions. A core group of bacterial families were identified in all gut regions with clear differences shown between the ileum and the various large intestine regions. The core in the ileum accounted for 32% of all sequences and comprised of only seven OTUs of varying abundance; the core in the large intestine was much smaller (5-15% of all sequences) with a much larger number of OTUs present but in low abundance. The most abundant member of the core community in the ileum was Lactobacillaceae, in the proximal large intestine the Lachnospiraceae and in the distal large intestine the Prevotellaceae. In conclusion, the presence of a core bacterial community in the large intestine of the horse that is made up of many low abundance OTUs may explain in part the susceptibility of horses to digestive upset.     

Changes in bacterial populations in the ileum of pigs fed low-phosphorus diets supplemented with different sources of fermentable carbohydrates

An experiment was conducted to evaluate the effects of differently fermentable carbohydrates on changes in bacterial populations in the ileum of growing pigs fed low-phosphorus (P) diets. Eight barrows (mean surgery BW 36 ± 0.9 kg) were fitted with simple T-cannulae at the distal ileum and were assigned to one of four dietary treatments: maize-soybean meal based control diet (CD), or 0.75 of CD supplemented with 0.25 lignocellulose, maize starch and high-methylated apple-pectin, respectively. Total bacterial cell counts as well as cell counts of Lactobacillus spp., Lactobacillus reuteri, Lactobacillus amylovorus/Lactobacillus sobrius, Lactobacillus mucosae, Enterococcus spp., Enterococcus faecium, Enterococcus faecalis, bifidobacteria, Clostridium coccoides cluster, Clostridium leptum cluster, Bacteroides–Prevotella–Porphyrmonas group and Enterobacteriaceae were determined by quantitative realtime PCR in DNA extracts of ileal digesta. Denaturing gradient gel electrophoresis (DGGE) of DNA fragments, generated by PCR targeting total or Lactobacillus spp. 16S rDNA, was used to estimate the bacterial diversity in the ileum. Lignocellulose supplementation tended (P<0.1) to increase cell counts of total bacteria in faeces compared with the control. Ileal bacterial populations responded differently to carbohydrate addition. Maize starch supplementation strongly stimulated the growth of total lactobacilli and Lactobacillus species (P≤0.05). Lignocellulose, in turn, enhanced the numbers of bifidobacteria, but reduced those of L. amylovorus compared with the control (P<0.05). Finally, pectin tended to increase the cell numbers of L. amylovorus/L. sobrius and the Bacteroides–Prevotella–Porphyrmonas group compared with the control (P<0.1). DGGE analysis revealed increased band numbers for total bacteria in the ileum of animals fed the lignocellulose and maize starch supplemented diets, while pectin reduced total bacterial (P<0.1) and Lactobacillus spp. diversity (P<0.05) compared with the control, as determined with the Shannon's index. Ileal VFA concentrations were decreased by pectin, while lignocellulose decreased faecal VFA concentrations. In conclusion, ileal bacterial populations and diversity are susceptible to changes in the carbohydrate composition of the diet. However, these changes were not related to major differences in the number of total bacteria in ileal digesta and faeces, but rather to changes in the bacterial species composition and their metabolic activity.     

Effects of sodium butyrate and salinomycin upon intestinal microbiota,mucosal morphology and performance of broiler chickens

The effect of dietary sodium butyrate (SB) or salinomycin (SAL) or both additives on performance, small intestinal morphology and microbial ecology of broiler chickens was studied. A growth trial was conducted with 96 Ross 308 female broilers from 1 to 30 days of age. Four treatment groups were fed with a non-supplemented control diet or three experimental diets supplemented with i) 300 mg SB (Adimix 30 coated) per kg, ii) 60 mg SAL (Sacox) per kg or iii) both additives in combination. Feed intake and body-weight gain decreased and gain-to-feed ratio increased due to SAL supplementation, while addition of SB did not affect performance in comparison with the control diet but positively affected feed intake and body-weight gain in comparison with birds fed the SAL-supplemented diet. Villus height in jejunum decreased, while crypt depth increased due to SAL supplementation. Addition of SB increased crypt depth in jejunum. No significant effect of either additive was observed in ileum morphology. Total short-chain organic acids concentration in ileal digesta decreased with SAL supplementation, mainly due to lower lactic acid concentration, but no effects were observed in the caeca. The SAL supplementation was accompanied by a pH increase in ileum and a pH decrease in caecum. No significant effect of SB addition was observed for these parameters. Total bacterial numbers and Lactobacillus [lactic acid bacteria (LAB)] counts in ileal and caecal contents were lower in birds fed with SAL-supplemented diet in comparison with birds fed with control or SB diet. DNA fingerprints revealed SAL supplementation to affect the microbial population by suppressing dominating LAB, potentially L. aviarius. The presented results show that dietary SAL, supplemented alone or in combination with SB, suppressed the microbial activity and altered the microbial community structure mainly in ileum. SAL alone negatively affected feed intake and body-weight gain; however, the effect was ameliorated by SB supplementation.     

Broiler chicken cecal microbiocenoses depending on mixed fodder

Molecular genetic techniques (NGS sequencing and quantitative PCR) were used to determine the composition of the cecal bacterial community of broiler chickens fed with different mixed fodder. The cecal microbiome exhibited taxonomic diversity, with both typical inhabitants of avian intestine belonging to the families Clostridiaceae, Eubacteriaceae, and Lactobacillaceae and to the phylum Bacteroidetes, and new unidentified taxa, as well as bacteria of the families Lachnospiraceae and Ruminococcaceae, which were previously considered restricted to the rumen microbiota. Contrary to traditional concepts, enterococci and bifidobacteria were among the minor components of the community, lactate-fermenting species were absent, and typical avian pathogens of the genus Staphylococcus were detected but seldom. Members of the family Suterellaceae and the genus Gallibacterium, which are responsible for avian respiratory infections, were also detected. Significant fluctuations of abundance and composition of microbial groups within the cecal community and of the parameters of broiler productivity were found to occur depending on the feed allowance. Cellulose content in the feed had the most pronounced effect on the composition and structure of bacterial communities. Decreased cellulose content resulted in a decrease of bacterial abundance by an order of magnitude and in increased ratios of members of the phylum Bacteroidetes and the family Clostridiaceae, which possess the enzymes degrading starch polysaccharides. Abundance of the normal inhabitants of avian intestine belonging to the genus Lactobacillus and the order Bacillales decreased, while the share of Escherichia and members of the family Sutterellaceae increased, including some species capable of causing dysbiotic changes in the avian intestine. No significant change in the abundance of cellulolytics of the families Ruminococcaceae, Lachnospiraceae, and Eubacteriaceae was observed.