Spatial and temporal variations of the bacterial community in the bovine digestive tract

Aims:  Improved knowledge of the bacterial community of the digestive tract is required to enhance the efficiency of digestion in herbivores. This work aimed to study spatial and temporal variations of the bacterial communities in the bovine digestive tract and their correlation with gut environmental parameters.
Methods and Results:  Rumen content and faeces of five cows were sampled for 3 weeks. In addition, reticulum content was sampled during the third week. Bacterial communities were assessed by studying capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) profiles of 16S rRNA genes. The bacterial community structure differed between the forestomach and faecal contents. The abundance of several operational taxonomic units changed from week to week. Bacterial community structure of the rumen was correlated to propionic acid and NH₃–N concentrations.
Conclusions:  The bacterial community of the bovine digestive tract varied in space and time.
Significance and Impact of the Study:  The study of the bacterial communities of the digestive tract in herbivores should be widened from the rumen to the large intestine. The amplitude and origin of the temporal variation of the ruminal bacterial community need to be better understood to improve the control of the fermentative activity in herbivores.     

Molecular monitoring of the developmental bacterial community in the gastrointestinal tract of Japanese infants

The dynamics of the developmental bacterial community in the Japanese neonatal gastrointestinal tract were examined by monitoring 16S ribosomal RNA gene (rDNA) diversity in fecal samples by PCR and denaturing gradient gel electrophoresis (DGGE). The results showed a certain pattern common in infants without antibiotic treatment, in which aerobes, e.g., Pseudomonas, appeared first and were then immediately replaced by facultative anaerobe, Enterococcus, Streptococcus, and Enterobacteriaceae through the first month, and finally strictly anaerobic Bifidobactrerium appeared.     

Molecular analysis of a bacterial chitinolytic community in an upland pasture

The effects of agricultural-improvement treatments on the chitinolytic activity and diversity of a microbial community were investigated within an upland pasture. The treatments of interest were lime and treated sewage sludge, both commonly applied to pasture land to improve fertility. Burial of chitin-containing litter bags at the field site resulted in enrichment of bacteria according to 16S rRNA fingerprinting. Chitinolytic-activity measurements showed that the highest activity occurred in those bags recovered from sludge-amended plots, which correlated well with increased counts of actinobacteria in samples from these chitin bags. Our findings suggest that sewage sludge increases the fertility of the soil in terms of chitinase activity. Ten clone libraries were constructed from family 18 subgroup A chitinases, PCR amplified from litter bags buried in soil in July 2000 or in September 2000, in a separate study. Analysis of these libraries by restriction fragment length polymorphism and sequencing showed that they were dominated by actinobacterium-like chitinase sequences. This suggests that actinobacteria have an important chitinolytic function in this soil ecosystem. Our findings showed that sludge application increased chitinolytic activity but decreased the diversity of chitinases present.     

Molecular analysis of bacterial community succession during prolonged compost curing

The compost environment consists of complex organic materials that form a habitat for a rich and diverse microbial community. The aim of this research was to study the dynamics of microbial communities during the compost-curing phase. Three different methods based on 16S rRNA gene sequence were applied to monitor changes in the microbial communities: (1) denaturing gradient gel electrophoresis of PCR-generated rRNA gene fragments; (2) partial rRNA gene clone libraries; and (3) a microarray of oligonucleotide probes targeting rRNA gene sequences. All three methods indicated distinctive community shifts during curing and the dominant species prevailing during the different curing stages were identified. We found a successional transition of different bacterial phylogenetic groups during compost curing. The Proteobacteria were the most abundant phylum in all cases. The Bacteroidetes and the Gammaproteobacteria were ubiquitous. During the midcuring stage, Actinobacteria were dominant. Different members of nitrifying bacteria and cellulose and macromolecule-degrading bacteria were found throughout the curing process. In contrast, pathogens were not detected. In the cured compost, bacterial population shifts were still observed after the compost organic matter and other biochemical properties had seemingly stabilized.     

Molecular profiling of bacterial species in the rabbit caecum

The diversity of bacteria present in the caecum of the rabbit was investigated. Partial bacterial 16S rRNA genes from a digested sample collected from the caecum of an adult rabbit were amplified by PCR. Sequence analysis of the amplified fragments indicated highest similarity was to bacterial sequences previously described from other gut environments. However, only one sequence showed significant identity (97% threshold) to any previously described bacterial 16S rRNA genes. Furthermore, most of the sequences clustered together in groups lacking representatives from sequences already described, suggesting that the rabbit caecal flora contains organisms not previously described.     

Molecular bacterial community analysis of clean rooms where spacecraft are assembled

Molecular bacterial community composition was characterized from three geographically distinct spacecraft-associated clean rooms to determine whether such populations are influenced by the surrounding environment or the maintenance of the clean rooms. Samples were collected from facilities at the Jet Propulsion Laboratory (JPL), Kennedy Space Flight Center (KSC), and Johnson Space Center (JSC). Nine clone libraries representing different surfaces within the spacecraft facilities and three libraries from the surrounding air were created. Despite the highly desiccated, nutrient-bare conditions within these clean rooms, a broad diversity of bacteria was detected, covering all the main bacterial phyla. Furthermore, the bacterial communities were significantly different from each other, revealing only a small subset of microorganisms common to all locations (e.g. Sphingomonas, Staphylococcus). Samples from JSC assembly room surfaces showed the greatest diversity of bacteria, particularly within the Alpha- and Gammaproteobacteria and Actinobacteria. The bacterial community structure of KSC assembly surfaces revealed a high presence of proteobacterial groups, whereas the surface samples collected from the JPL assembly facility showed a predominance of Firmicutes. Our study presents the first extended molecular survey and comparison of NASA spacecraft assembly facilities, and provides new insights into the bacterial diversity of clean room environments .     

Molecular analysis of the bacterial community in a continental high-temperature and water-flooded petroleum reservoir

Water from a continental high-temperature, long-term water-flooded petroleum reservoir in Huabei Oilfield in China was analysed for its bacterial community and diversity. The bacteria were characterized by their 16S rRNA genes. A 16S rRNA gene clone library was constructed from the community DNA, and using restriction fragment length polymorphism analysis, 337 randomly selected clones were clustered with 74 operational taxonomic units. Sequencing and phylogenetic analyses showed that the screened clones were affiliated with Gammaproteobacteria (85.7%), Thermotogales (6.8%), Epsilonproteobacteria (2.4%), low-G+C Gram-positive (2.1%), high-G+C Gram-positive, Betaproteobacteria and Nitrospira (each <1.0%). Thermopilic bacteria were found in the high-temperature water from the flooded petroleum reservoir, as well as mesophilic bacteria such as Pseudomonas-like clones. The mesophilic bacteria were probably introduced into the reservoir as it was being exploited. This work provides significant information on the structure of bacterial communities in high-temperature, long-term water-flooded petroleum reservoirs.     

Lactobacillus cells in the rabbit digestive tract and the factors affecting their distribution

Lactobacillus fermentum was present in small numbers in the caecum and colon of only one of 16 rabbits. Studies aimed at elucidating the factors affecting the colonization of lactobacilli in rabbit gut were thus performed. These studies included investigation of the effect of gastric juice and bile salts on the viability of lactobacilli, assay of the survival rates of lactobacilli in the gastrointestinal tracts of the rabbits with or without ileum cannulation and measurement of the adhesive capability of lactobacilli to the rabbit intestinal epithelial cells. Results showed that, although some lactobacilli were resistant to the rather low pH levels of rabbit gastric juice, lack of adhesive capability may prevent them from colonizing in the intestinal tract. Therefore, if lactobacilli are to be used as probiotics for rabbit, factors that affect their viability and ability to colonize should be considered.     

Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis

Thirty microbial phylotypes of microorganisms were found in the gastrointestinal tract of chicken belonging to the Hajseks White breed, and 38 phylotypes were found in the gastrointestinal tract of chicken belonging to the Hajseks Brown breed. The microbiome of the gastrointestinal tract of the chicken embryos of the Hajseks White breed was dominated by the typical representatives of avian intestinal microflora—bacteria of the family Enterobacteriaceae (47.3%), orders Actinomycetales (13.6%) and Bifidobacteriales (20.6%), and the family Lachnospiraceae (1.1%). The microbiome of the gastrointestinal tract of the chicken embryos of the Hajseks Brown breed was dominated by the pathogenic bacteria of the order Rickettsiales (94.8%). The metagenome of gastrointestinal tract of both breeds also contained a small number of genes of unidentified bacteria.     

Chitinolytic enzymes and the bacterial microflora in the digestive tract of cod, Gadus morhua

The levels of chitinolytic enzymes and chitinolytic bacteria in the digestive tract of feeding and fasting cod were compared. Enzyme activities within a given tissue were of a similar order irrespective of the presence of chitinolytic bacteria and/or chitin. Cod chitinase and chitobiase are therefore endogenous and constitutive enzymes. Fasting cod had similar numbers of bacteria within the gastro-intestinal compartments as feeding fish. Representative bacterial isolates from fasting fish were characterized.     

Molecular analysis of halophilic bacterial community for high-rate denitrification of saline industrial wastewater

A denitrification system for saline wastewater utilizing halophilic denitrifying bacteria has not been developed so far. In this study, denitrification performance and microbial community under various saline conditions were investigated using denitrifying sludge acclimated under low-salinity condition for a few years as seed sludge. A continuous denitrification experiment showed that denitrification performance and microbial community at 10% salinity was higher than that at 1% salinity. The microbial community in the denitrification sludge that was acclimated under low salinity was monitored by terminal-restriction fragment length polymorphism (T-RFLP) analysis during acclimation to high-salinity condition. T-RFLP profiles and clone analysis based on 16S rRNA-encoding genes in the sludge of the denitrification system with 10% salinity indicated that the γ-Proteobacteria, particularly Halomonas spp., were predominant species, suggesting that these bacterial members were possibly responsible for a high denitrification activity under high-salinity conditions. Furthermore, the investigation of denitrification performance under various saline conditions revealed that 4–10% salinity results in the highest denitrification rate, indicating that this salinity was optimal for predominant bacterial species to exhibit denitrification activity. These results indicate the possibility that an appropriate denitrification system for saline wastewater can be designed using acclimated sludge with a halophilic community.     

Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures

Bacterial community structure and diversity in rhizospheres in two types of grassland, distinguished by both plant species and fertilization regimen, were assessed by performing a 16S ribosomal DNA (rDNA) sequence analysis of DNAs extracted from triplicate soil plots. PCR products were cloned, and 45 to 48 clones from each of the six libraries were partially sequenced. Phylogenetic analysis of the resultant 275 clone sequences indicated that there was considerable variation in abundance in replicate unfertilized, unimproved soil samples and fertilized, improved soil samples but that there were no significant differences in the abundance of any phylogenetic group. Several clone sequences were identical in the 16S rDNA region analyzed, and the clones comprised eight pairs of duplicate clones and two sets of triplicate clones. Many clones were found to be most closely related to environmental clones obtained in other studies, although three clones were found to be identical to culturable species in databases. The clones were clustered into operational taxonomic units at a level of sequence similarity of >97% in order to quantify diversity. In all, 34 clusters containing two or more sequences were identified, and the largest group contained nine clones. A number of diversity, dominance, and evenness indices were calculated, and they all indicated that diversity was high, reflecting the low coverage of rDNA libraries achieved. Differences in diversity between sample types were not observed. Collector's curves, however, indicated that there were differences in the underlying community structures; in particular, there was reduced diversity of organisms of the alpha subdivision of the class Proteobacteria (alpha-proteobacteria) in improved soils.     

Molecular analysis of autochthonous microbiota along the digestive tract of juvenile grouper Epinephelus coioides following probiotic Bacillus pumilus administration

Aims: To evaluate the diversity of dominant autochthonous microbiota along the digestive tract of juvenile Epinephelus coioides following the dietary administration of probiotic Bacillus pumilus for 60 days. Methods and Results: Polymerase chain reaction‐denaturing gradient gel electrophoresis (PCR‐DGGE) with subsequently sequencing analysis was used to assess the gut microbiota. Generally similar DGGE patterns were observed in the foregut, midgut and hindgut of E. coioides, while the similarity dendrogram clearly revealed three different clusters depending on the three compartments of the GI tract. Dietary administration of B. pumilus stimulated its colonization in each compartment of the digestive tract. Samples collected from the probiotic group and the control group showed similar DGGE patterns, and no significant difference in the total number of bands and the Shannon index were detected between the probiotic group and the control group, suggested that B. pumilus exert no significant effect on the gut microbiota. However, various potentially beneficial bacteria, such as uncultured Bacillus sp. clone QJNY94‐like, Nitratireductor sp. YCSC5‐like, Methylobacterium hispanicum‐like and Microbacterium sp. YACS1‐like bacteria were stimulated by probiotic B. pumilus, while the potential harmful Staphylococcus saprophyticus‐like bacterium was depressed. Conclusions: Autochthonous gut microbiota of E. coioides was modulated to some degree, not significant, by probiotic B. pumilus, various potentially beneficial bacteria were selectively stimulated, while one potential harmful species was depressed. Significance and Impact of the Study: This work represents the first report that dietary administration of probiotic B. pumilus modulated the gut microbiota of E. coioides. These findings broaden our understanding of probiotic effects at the gut level, which is helpful in understanding the mechanisms that underpin host benefits.     

Probiotics shown to change bacterial community structure in the avian gastrointestinal tract.

Culturing and molecular techniques were used to monitor changes in the bacterial flora of the avian gastrointestinal (GI) tract following introduction of genetically modified (GM) and unmodified probiotics. Community hybridization of amplified 16S ribosomal DNA demonstrated that the bacterial flora of the GI tract changed significantly in response to the probiotic treatments. The changes were not detected by culturing. Although both GM and non-GM strains of Enterococcus faecium NCIMB 11508 changed the bacterial flora of the chicken GI tract, they did so differently. Probing the community DNA with an Enterococcus faecalis-specific probe showed that the relative amount of E. faecalis in the total eubacterial population increased in the presence of the non-GM strain and decreased in the presence of the GM probiotic compared with the results obtained with an untreated control group.     

Bifidobacteria in the digestive tract of bumblebees

Bifidobacteria and other bacterial groups (lactobacilli, facultative anaerobes, anaerobes) from the digestive tract of three bumblebee species (Bombus lucorum (34 samples), Bombus pascuorum (18 samples) and Bombus lapidarius (9 samples)) were enumerated and characterised. Counts of facultative anaerobic bacteria and lactobacilli (5.41 ± 2.92 and 2.69 ± 3.02 log CFU/g of digestive tract content) were lower than those of anaerobes (7.66 ± 0.86 log CFU/g). Counts of bifidobacteria were determined using two selective media: MTPY (Modified Trypticase Phytone Yeast extract agar) and a new medium with pollen extract. There was no significant difference between the counts of bifidobacteria from both media, 5.00 ± 2.92 log CFU/g on MTPY and 5.00 ± 2.87 on the pollen medium. Subsequently, 187 bacterial strains of the family Bifidobacteriaceae (fructose-6-phosphate phosphoketolase-positive) were isolated from three different localities and from all three species of bumblebees. Bifidobacteria were found in 42 out of 61 specimens (69%). Twenty-three (38%) specimens had counts of bifidobacteria higher than 7.0 log CFU/g. Bifidobacteria represented the dominant group of anaerobes (>70% of total anaerobes), i.e., the principal group of bacteria in the bumblebee digestive tract, in only fourteen specimens (23% of total). For the first time, bifidobacteria were isolated from the digestive tract of bumblebees. In addition, we suggest, on the basis of biochemical tests (API 50 CHL and RAPID ID 32) and genetic methods (PCR and DGGE), that these bacteria may represent new species within the family of Bifidobacteriaceae.