Quantification of total bacteria, enterobacteria and lactobacilli populations in pig digesta by real-time PCR

Use of mannanoligosaccharides and zinc chelate as growth promoters and diarrhea preventative in weaning pigs: Effects on microbiota and gut function1

The efficacy of a commercial source of mannanoligosacharides (BM), organic zinc (BP), or their combination to enhance performance, gastrointestinal health, and immune response in weaned pigs was evaluated. A total of 128 piglets, weaned at 20 +/- 2 d, were housed in 32 pens. Animals received 1 of 4 dietary treatments: a control diet (CT) to which 0.2% of BM, 80 mg/kg of Zn as BP, or both additives (BMP) were added. The experiment lasted for 5 wk including a prestarter period of 2 wk and a starter period of 3 wk. Body weight was recorded and daily feed intake was calculated. Fecal consistency was monitored for the first 21 d. After 2 wk, 32 animals were killed, digesta samples from the stomach, ileum, and cecum were collected, and pH and the short-chain fatty acid profile were determined. Microbiological counts for enterobacteria and lactobacilli were evaluated using quantitative PCR. Histological parameters in the jejunum and immunoglobulin concentrations in serum and ileal digesta were also measured. Both additives improved G:F during the starter period (0.63, 0.69, 0.67, and 0.68 for CT, BM, BP, and BMP, respectively; P < 0.04). Mean fecal score values for the first 21 d were improved by BM and BP, showing decreased values compared with the CT diet (1.22, 0.89, 0.87, and 1.06 for CT, BM, BP, and BMP, respectively; P = 0.002). The addition of BM decreased enterobacteria counts in the jejunum (9.13, 8.05, 8.87, and 7.89 log 16S rRNA gene copies/g of matter for CT, BM, BP, and BMP, respectively; P = 0.05). Empty ileal weight, defined as the segment including the continuous Peyer's patch, tended (P = 0.08) to increase with BP treatment (8.9, 9.6, 11.9, and 10.3 g/kg of BW for CT, BM, BP, and BMP, respectively). Crypt depths in the jejunum were lower in animals fed the combination of the additives (BPM) compared with those fed the control diet (281 vs. 235; P < 0.03). No significant differences were registered in pH, short-chain fatty acids, or serum and ileal immunoglobulin concentrations. The results suggest that the use of BM or BP can improve the efficiency of gain during the starter period.

A rapid method for detecting and quantifying bacterial DNA in rust fungal DNA samples

Bacterial DNA contamination of rust fungal DNA can be a significant problem for sequencing the rust fungus. Sequence assembly is much more difficult if the sequence contigs are mixed with bacterial sequence. A quantitative real-time polymerase chain reaction (qPCR) assay was developed to quantify bacterial DNA within rust fungal DNA samples and the results were compared with those obtained from traditional CFU counts. Real-time PCR showed higher values of DNA contamination than CFU. However, the ranking of samples from low to high for bacterial contamination was consistent between the methods. Reasons for the differences between the methods are discussed. The qPCR assay was tested by adding known quantities of Escherichia coli DNA to Puccinia graminis DNA samples. The assay reliably quantified bacterial contamination at > or = 1.0% of the total sample DNA. When bacterial contamination was <1.0%, fungal DNA also occasionally was amplified, nullifying the quantification measurement. However, primer specificity was not simply the product of the ratio of bacterial DNA to fungal DNA. Bacterial contamination could be quantified below 1.0% if the bacterial DNA concentration was approximately 70 pg/mul or greater. Therefore, spiking the fungal samples with a known concentration of E. coli bacterial DNA successfully eliminated the amplification of fungal DNA, making quantification of contaminating bacterial DNA possible for samples with low contamination levels.

Characterization of the gastrointestinal mucosa-associated microbiota of pigs and chickens using culture-based and molecular methodologies

The microbiota of the gastrointestinal tract (GIT) can play an important role in the healthy status of farm animals and in the safety of the whole food chain. In this study, the mucosa-associated microbiota of the GIT of pigs and chickens was analyzed by culture methods and fluorescence in situ hybridization combined with flow cytometry (FCM-FISH). In all pig GIT sections, lactic acid bacteria, Enterobacteriaceae, Atopobium, Bacteroides, and Clostridium histolyticum were the predominant bacterial groups. Atopobium, Bifidobacterium, Bacteroides, and Lactobacillus were detected at higher levels (P < 0.05) in the intestine than in the stomach. In all broilers' GIT sections, lactic acid bacteria, Atopobium, Bacteroides, and Escherichia coli were the predominant bacterial groups. Atopobium, Bifidobacterium, E. coli, and Eubacterium rectale--Clostridium coccoides counts were significantly higher (P < 0.05) in the crop, while those of Bacteroides and Lactobacillus were higher (P < 0.05) in the large intestine. Lactic acid bacteria were one of the predominant GIT mucosa-associated bacteria of pigs and broilers, which could be an index of their healthy status. FCM-FISH analysis also allowed the detection of bacterial groups hard to cultivate yet quantitatively important. The distribution of Lactobacillus and Bacteroides followed the same trend in both animal species, whereas that of Atopobium and Bifidobacterium was the opposite. These results contribute to the knowledge on the diversity and distribution of the animal GIT mucosa-associated microbiota.

Changes in caecal microbiota and mucosal morphology of weaned pigs

An experiment was designed to monitor the changes in caecal microbiota associated with early weaning. Twelve piglets (20+/-2 days) from six different litters were selected from a commercial source. For the two experimental groups, one animal from each litter was weaned onto a post-weaning diet (W) and the other remained with the sow (S). After 1 week, animals were sacrificed and caecal samples taken. Microbial counts for total bacteria, enterobacteria and lactobacilli populations were determined by quantitative PCR using SYBR Green dye. Microbial profiles were assessed by terminal restriction fragment length polymorphism (t-RFLP). Weaning promoted an increase in the enterobacteria:lactobacilli ratio (0.27 versus 1.67 log/log 16S rRNA gene copy number, P=0.05). Total bacteria and richness of the caecal microbial ecosystem (number of peaks) were similar in both experimental groups (49.3 for S and 53.4 for W, respectively, P=0.22), although the band patterns were clearly grouped in two different clusters by dendogram analysis. Weaning was also associated with a decrease in crypt density, an increase in mytotic index and a decrease in the number of goblet cells. A reduced immunological response was also observed and was manifested by an increase in intraepithelial lymphocytes and lymphocyte density in the lamina propria. Weaning appears to be critical in the establishment of the caecal microbiota in pigs with important changes, particularly in microbial groups and in caecal mucosal architecture.

Gene expression of commensal Lactobacillus johnsonii strain NCC533 during in vitro growth and in the murine gut

Work with pathogens like Vibrio cholerae has shown major differences between genes expressed in bacteria grown in vitro and in vivo. To explore this subject for commensals, we investigated the transcription of the Lactobacillus johnsonii NCC533 genome during in vitro and in vivo growth using the microarray technology. During broth growth, 537, 626, and 277 of the 1,756 tested genes were expressed during exponential phase, "adaptation" (early stationary phase), and stationary phase, respectively. One hundred one, 150, and 33 genes, respectively, were specifically transcribed in these three phases. To explore the in vivo transcription program, we fed L. johnsonii containing a resistance plasmid to antibiotic-treated mice. After a 2-day washout phase, we determined the viable-cell counts of lactobacilli that were in the lumina and associated with the mucosae of different gut segments. While the cell counts showed a rather uniform distribution along the gut, we observed marked differences with respect to the expression of the Lactobacillus genome. The largest number of transcribed genes was in the stomach (n = 786); the next-largest numbers occurred in the cecum (n = 391) and the jejunum (n = 296), while only 26 Lactobacillus genes were transcribed in the colon. In vitro and in vivo transcription programs overlapped only partially. One hundred ninety-one of the transcripts from the lactobacilli in the stomach were not detected during in vitro growth; 202 and 213 genes, respectively, were transcribed under all in vitro and in vivo conditions; but the core transcriptome for all growth conditions comprised only 103 genes. Forty-four percent of the NCC533 genes were not detectably transcribed under any of the investigated conditions. Nontranscribed genes were clustered on the genome and enriched in the variable-genome part. Our data revealed not only major differences between in vitro- and in vivo-expressed genes in a Lactobacillus gut commensal organism but also marked changes in the expression of genes along the digestive tract.

Quantification of mucosa-adhered microbiota of lambs and calves by the use of culture methods and fluorescent in situ hybridization coupled with flow cytometry techniques

The intestinal mucosa-associated microbiota could play important biological roles due to its close proximity with the animal host, but knowledge on its composition is still limited. The aim of this study was to characterize the microbial communities tightly associated with different parts (rumen, duodenum and colon) of the gastrointestinal tract (GIT) of healthy lambs and calves by using both cultural, and fluorescent in situ hybridization-flow cytometry (FCM-FISH) techniques. Lactic acid bacteria genera were one of the predominant bacteria detected in lambs and calves by both methodologies, possibly constituting an index of their healthy status. The levels of Lactobacillus were significantly higher (p<0.05) in the rumen and duodenum of lambs, and in the rumen of calves. The levels of Bifidobacterium were significantly higher (p<0.05) in the colon of both animal species and the rumen of lambs. Significant differences (p<0.05) were found in counts of other microbial groups (yeast, Enterococcus, Propionibacterium, Bacteroides, Clostridium and Enterobacteriaceae) at diverse GI sections depending on the animal species. In general, microbial counts follow the same trends regardless the applied technique. The most remarkable differences were found in detection levels of Bacteroides and Clostridium, which tended to be significantly higher (p<0.05) when analysed by FCM-FISH. This technique also allowed the detection of quantitatively important bacteria (sulphate-reducing bacteria, Atopobium and Coriobacterium), which are difficult to cultivate in selective medium. Therefore, FCM-FISH has been proven to be a sensitive high throughput approach that provides additional information to that obtained by traditional culture techniques about the complexity of the GI ecosystem of these animal species.

Novel methods of quantitative real-time PCR data analysis in a murine Helicobacter pylori vaccine model

Monitoring of Helicobacter pylori in the stomach is important to assess the efficacy of new vaccines against the pathogen. To realise the full potential of quantitative real-time PCR (q-PCR), this technology has to offer accurate and easy models of post-PCR data analysis. In this work, we used a variety of absolute and relative approaches of q-PCR data analysis to monitor the H. pylori infection in the stomach of immunized mice. Relative quantification was performed with Ct-based methods, with the DART program, and with two methods based on the mathematical analysis of raw fluorescence kinetics, the LinReg program and the Sigmoidal Curve Fitting Method. The different calculation methods were validated in mice immunized with cell lysates of Lactococcus lactis expressing the H. pylori urease subunit B in combination with cholera toxin. The H. pylori load was found to be reduced in immunized mice by a factor of 50-144, depending on the calculation method employed. We found that relative quantification using DART, LinReg and Sigmoidal Curve Fitting methods generated similar results (infection ratios of 54-58) with absolute quantification results (54-65). Results were very different to those using relative quantification Ct-based methods without a correction for PCR efficiency (ratio of 92-144) and with results based on conventional culture method (ratio of 34). Overall, this study demonstrates that q-PCR associated with a relative quantification analysis is a powerful tool for the monitoring of microorganisms in tissue. It could be used as an alternative to standard curve approach especially for the investigation of microbial load in vaccine models.

A proportional analysis method using non-kinetic real-time PCR

Prompted by increasing interest in proportional analysis of genetic types, we developed a simple assay technique for determining the ratio of a specific target gene in the total genes that can be amplified with the same PCR primer. The key feature of this method is that the following two tasks are performed in a single-tube real-time PCR system: task 1, PCR amplification of the total genes including the target using a labeled PCR primer, with concurrent monitoring of the total copy number of the PCR product; task 2, detection of the signal of the target gene at each cycle of amplification, using a labeled nucleotide probe. In principle, the ratio of the target gene to the total genes is represented by the signal detected in 'task 2' at the cycle in which the PCR product reached a prescribed copy number (assessed by 'task 1').