Effect of mannanoligosaccharides supplementation on caecal microbial activity of rabbits

A total of 200 weaned (35 days) hybrid Hyla rabbits were randomly divided among five groups housed in bicellular cages (20 cages per group). Between 35 and 60 days of age, the groups were submitted to the following treatments: group ANT (positive control) fed a basal diet supplemented with antibiotics (colistin sulphate, 144 mg/kg; tylosin, 100 mg/kg; and oxytetracyclin, 1000 mg/kg); groups MOS_0.5, MOS_1.0 and MOS_1.5 fed the basal diet supplemented with 0.5, 1.0 and 1.5 g/kg mannanoligosaccharides (MOS), respectively; another group fed the basal diet without antibiotics or mannanoligosaccarides supplementation (negative control). Along the trial, an episode of epizootyc rabbit enteropathy occurs so that in the control group mortality rate was very high (78%) and survivor rabbits showed severe symptoms of disease (diarrhoea). Thus, the control group was discarded from the trial. At 60 days of age, samples of caecal content were collected from 10 rabbits per group and used as inocula for an in vitro gas production trial. At the end of fermentation (120 h of incubation), organic matter digestibility (OMd), cumulative gas production, fermentation kinetics, pH, volatile fatty acid (VFA) and NH3 productions were measured. Inoculum from MOS_1.0 rabbits showed the significant higher values of OMd (64.21%, P < 0.05), gas production (262.32 ml/g, P < 0.05), acetate (96.99 mmol/g OM, P < 0.05) and butyrate (26.21 mmol/g OM, P < 0.05) than the other groups. Slight differences were recorded among the groups ANT, MOS_0.5 and MOS_1.5. In addition, branched chain acids, in proportion to total VFAs, were significantly higher in MOS_1.0 inoculum (0.04, P < 0.05). MOS are able to affect fermentation activity of caecal micro-organism, but their activities seem not proportional to their level in the diet.     

Biodiversity of soil microbial communities in agricultural systems

The productivity and health of agricultural systems depend greatly upon the functional processes carried out by soil microorganisms and soil microbial communities. The biodiversity of the soil microbial communities and the effect of diversity on the stability of the agricultural system, is unknown. Taxonomic approaches to estimating biodiversity of soil microbial communities are limited by difficulties in defining suitable taxonomic units and the apparent non-culturability of the majority of the microbial species present in the soil. Analysis of functional diversity may be a more meaningful approach but is also limited by the need to culture organisms. Approaches which do not rely on culturing organisms such as fatty acid analysis and 16S/18S rRNA analysis have provided an insight into the extent of genetic diversity within communities and may be useful in the analysis of community structure. Scale effects, including successional processes associated with organic matter decomposition, local effects associated with abiotic soil factors, and regional effects including the effect of agricultural management practices, on the diversity of microbial communities are considered. Their impact is important in relation to the minimum biodiversity required to maintain system function.     

Biodiversity in microbial communities: system scale patterns and mechanisms

The relationship between anthropogenic impact and the maintenance of biodiversity is a fundamental question in ecology. The emphasis on the organizational level of biodiversity responsible for ecosystem processes is shifting from a species-centred focus to include genotypic diversity. The relationship between biodiversity measures at these two scales remains largely unknown. By stratifying anthropogenic effects between scales of biodiversity of bacterial communities, we show a statistically significant difference in diversity based on taxonomic scale. Communities with intermediate species richness show high genotypic diversity while speciose and species-poor communities do not. We propose that in species-poor communities, generally comprising stable yet harsh conditions, physiological tolerance and competitive trade-offs limit both the number of species that occur and the loss of genotypes due to decreases in already constrained fitness. In species-rich communities, natural environmental conditions result in well-defined community structure and resource partitioning. Disturbance of these communities disrupts niche space, resulting in lower genotypic diversity despite the maintenance of species diversity. Our work provides a model to inform future research about relationships between species and genotypic biodiversity based on determining the biodiversity consequences of changing environmental context.     

Comparative in vitro study of caecal microbial activity in brown hares and domestic rabbits which were offered the same diet

The products of the microbial activity in the large intestine are an important source of energy for herbivores. A previous study showed differences in caecal methanogenesis and short-chain fatty acid (SCFA) profiles between brown hares and domestic rabbits. The present study was performed on animals which were offered the same diet to eliminate the impact of diet on the comparative analyses of microbial metabolites. Caecal samples of hares and rabbits were incubated in triplicate, i.e. without any supplementary substrate (control) or with the addition of wheat bran or oat bran. Calculated as percentage of body weight, the stomachs of the rabbits were heavier than those of the hares, but caeca of the hares weighed more than those of the rabbits. The total SCFA concentration in caecal samples was higher in rabbits than in hares, and it increased in both species when the supplementary fermentation substrates were added. In hares, the molar proportion of propionate was higher and that of butyrate was lower compared to rabbits. The addition of substrate decreased acetate and propionate but increased the molar proportion of butyrate. Microbial fermentation resulted in greater gas release in rabbit caecal samples compared to those of hares. Methanogenesis tended to be lower in hares than in rabbits, but high individual variability was observed, especially in hares. Our study stated lower microbial activity in the caeca of brown hares compared to domestic rabbits. The presented results might lead to assumption that differences between fermentation patterns were not caused by diet but resulted from the peculiarities of both species.     

Effects of low dietary protein on the metabolites and microbial communities in the caecal digesta of piglets

Thirty-six healthy piglets (weighing 10 ± 1 kg; three animals per pen) were randomly allocated to two treatments: (i) a low protein diet (14% crude protein [CP]) supplemented with lysine, methionine, threonine and tryptophan (Group LP) and (ii) a normal protein diet (20% CP, Group NP), resulting in six replicate pens per treatment. One piglet from each pen was slaughtered at days 10, 25 and 45 of the experiment. For the whole experimental period of 45 d, Group LP had lower feed intake and daily gain and a higher feed-to-gain ratio compared with Group NP. At day 10, no effects on measured caecum metabolites were observed, but at days 25 and 45 in Group LP the concentration of ammonia-N, cadaverine, branched chain fatty acids and acetate were reduced. This was also true for the concentration of short chain fatty acids at day 45. The results of denaturing gradient gel electrophoresis showed that microbial diversity in Group LP was less abundant at day 25, but there was no difference at days 10 and 45. An unweighted pair group mean average analysis showed that the similarities were lower between Groups LP and NP at day 10 and higher at days 25 and 45. Quantitation results indicated that the numbers of Firmicutes and Clostridium cluster IV were lower in Group LP than in Group NP at day 25, but there were no differences at days 10 and 45. In conclusion, the low protein diet markedly reduced the metabolites of protein and carbohydrate fermentation and altered microbial communities in the caecal digesta of piglets.     

Macrofilamentous microbial communities in the metal-rich and acidic River Tinto, Spain

A novel type of macroscopic microbial community consisting of large dendritic filaments (up to 1.5 m) in a pH 2.0 dam of the River Tinto (South-western Spain) is described. The combined use of 16S rRNA-gene surveys and fluorescent in situ hybridisation (FISH) suggested that gamma-proteobacteria and a relative large diversity of alpha-proteobacteria dominated these structures. beta-Proteobacteria, Actinobacteria and Firmicutes were also detected. Whereas acidophilic bacteria of the genera Acidithiobacillus, Leptospirillum and Acidiphilium, and archaea belonging to the Thermoplasmatales dominate mine acid drainage waters and streamers (riverbed filamentous biofilms), none of the lineages identified in this study affiliate to typical acid mine drainage acidophilic bacteria. Bacteria of the Tinto macrofilaments might be heterotrophic, and could be feeding on the organic matter entrapped in the filamentous structure.     

Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities

Background

Host-associated microbes comprise an integral part of animal digestive systems and these interactions have a long evolutionary history. It has been hypothesized that the gastrointestinal microbiome of humans and other non-human primates may have played significant roles in host evolution by facilitating a range of dietary adaptations. We have undertaken a comparative sequencing survey of the gastrointestinal microbiomes of several non-human primate species, with the goal of better understanding how these microbiomes relate to the evolution of non-human primate diversity. Here we present a comparative analysis of gastrointestinal microbial communities from three different species of Old World wild monkeys.

Methodology/Principal Findings

We analyzed fecal samples from three different wild non-human primate species (black-and-white colobus [Colubus guereza], red colobus [Piliocolobus tephrosceles], and red-tailed guenon [Cercopithecus ascanius]). Three samples from each species were subjected to small subunit rRNA tag pyrosequencing. Firmicutes comprised the vast majority of the phyla in each sample. Other phyla represented were Bacterioidetes, Proteobacteria, Spirochaetes, Actinobacteria, Verrucomicrobia, Lentisphaerae, Tenericutes, Planctomycetes, Fibrobacateres, and TM7. Bray-Curtis similarity analysis of these microbiomes indicated that microbial community composition within the same primate species are more similar to each other than to those of different primate species. Comparison of fecal microbiota from non-human primates with microbiota of human stool samples obtained in previous studies revealed that the gut microbiota of these primates are distinct and reflect host phylogeny.

Conclusion/Significance

Our analysis provides evidence that the fecal microbiomes of wild primates co-vary with their hosts, and that this is manifested in higher intraspecies similarity among wild primate species, perhaps reflecting species specificity of the microbiome in addition to dietary influences. These results contribute to the limited body of primate microbiome studies and provide a framework for comparative microbiome analysis between human and non-human primates as well as a comparative evolutionary understanding of the human microbiome.     

Evolutionary relationships of wild hominids recapitulated by gut microbial communities

Multiple factors over the lifetime of an individual, including diet, geography, and physiologic state, will influence the microbial communities within the primate gut. To determine the source of variation in the composition of the microbiota within and among species, we investigated the distal gut microbial communities harbored by great apes, as present in fecal samples recovered within their native ranges. We found that the branching order of host-species phylogenies based on the composition of these microbial communities is completely congruent with the known relationships of the hosts. Although the gut is initially and continuously seeded by bacteria that are acquired from external sources, we establish that over evolutionary timescales, the composition of the gut microbiota among great ape species is phylogenetically conserved and has diverged in a manner consistent with vertical inheritance.     

Nutritional and sanitary statuses alter postweaning development of caecal microbial activity in the rabbit

The postweaning development of caecal microbial activity was studied in the rabbit according to the sanitary status (conventional "C" vs. specified pathogen-free "SPF") and the nutritional status (standard-fibre "SF" vs. deficient-fibre "DF" diet). The two diets were distributed ad libitum from weaning (28 days) to 70 days of age, respectively, to 80 C and 72 SPF rabbits. From 28 to 42 days, the volatile fatty acids concentration in the caecum (tVFA) of C rabbits was 50 mM/L and increased by 46% between 42 and 56 days, without interactions with the diet effect. In parallel, the bacterial fibrolytic activity decreased for xylanase and CMCase (-32% and -60%, respectively, P<0.05), while pectinase activity decreased more regularly from 28 to 70 days (-28%, P<0.05). At weaning, tVFA was similar among C or SPF rabbits, while at 70 days, it decreased by 23% for SPF and increased in C group (+31%). Cellulasic and hemicellulasic activity of bacteria were two to three times lower, respectively, in SPF rabbits compared to conventional ones. No interaction was detected between sanitary and nutritional status at 70 days of age for the caecal fermentative activity. With the FD diet, tVFA decreased by 10%, while butyrate proportion increased by 37% (at 70 days), whatever the sanitary status. In 70-day-old rabbits (C or SPF group), pectinasic activity was reduced by 30% when rabbits were fed the FD compared to the SF one.     

Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures

We have begun to examine the basis for incongruence between hot spring microbial mat populations detected by cultivation or by 16S rRNA methods. We used denaturing gradient gel electrophoresis (DGGE) to monitor enrichments and isolates plated therefrom. At near extincting inoculum dilutions we observed Chloroflexus-like and cyanobacterial populations whose 16S rRNA sequences have been detected in the New Pit Spring Chloroflexus mat and the Octopus Spring cyanobacterial mat. Cyanobacterial populations enriched from 44 to 54°C and 56 to 63°C samples at near habitat temperatures were similar to those previously detected in mat samples of comparable temperatures. However, a lower temperature enrichment from the higher temperature sample selected for the populations found in the lower temperature sample. Three Thermus populations detected by both DGGE and isolation exemplify even more how enrichment may bias our view of community structure. The most abundant population was adap ted to the habitat temperature (50°C), while populations adapted to 65°C and 70°C were 102- and 104-fold less abundant, respectively. However, enrichment at 70°C favored the least abundant strain. Inoculum dilution and incubation at the habitat temperature favored the more numerically relevant populations. We enriched many other aerobic chemoorganotropic populations at various inoculum dilutions and substrate concentrations, most of whose 16S rRNA sequences have not been detected in mats. A common feature of numerically relevant cyanobacterial, Chloroflexus-like and aerobic chemorganotrophic populations, is that they grow poorly and resist cultivation on solidified medium, suggesting plating bias, and that the medium composition and incubation conditions may not reflect the natural microenvironments these populations inhabit.     

Stress-induced inhibition of the ileal, caecal, and colonic contractile activity in rabbits]

In alert rabbits, immobilisation stress decreased the spike burst rate and amplitude in ileum, caecum, and colon for 20 min. Following beta-adrenoceptor blockade, the contractile activity suppression was aggravated. The stress seems to lead to suppression of the ileal, caecal, and colonic contractile activity for up to 40 min which is unrelated to adrenergic inhibition of the smooth muscle activity mediated by beta-adrenoceptors.     

Bluetongue epidemiology in wild ruminants from Southern Spain

Serum samples from 210 wild ruminants collected between 2006 and 2007 in southern Spain were tested for antibodies against bluetongue virus (BTV) by means of a competitive ELISA assay. Eighty-seven of the 210 wild ruminants analysed (41%) showed antibodies against BTV. Statistically significant differences were found in the seroprevalence among species: 66% (65 of 98) for red deer (Cervus elaphus), 50% (ten of 20) for fallow deer (Dama dama), 33% (three of nine) for mouflon (Ovis aries musimon) and 11% (nine of 83) for Spanish ibex (Capra pyrenaica). Overall, the sites where seropositive wild ruminants were found coincide with the areas where BTV had been detected in livestock, but in eastern Sierra Morena, the virus circulated in wild ruminants, although it had not been detected in domestic ruminants in the same areas. Wild ruminants over 1-year of age (sub-adults and adults) had significantly higher seroprevalences than juvenile animals. Statistically significant differences were also observed between BTV seroprevalence and management (free-ranging vs. captivity) with higher prevalence in free-ranging animals. The high seroprevalences obtained suggest that BTV is widespread in wild ruminants in southern Spain. This factor could have an important influence on the evolution of the infection in domestic livestock and indicates the need to include wild ruminant species in BTV surveillance or control programs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray

Microarray technology was used to characterize and compare hexachlorocyclohexane (HCH) contaminated soils from Spain. A library of 2,290 hypervariable 16S rRNA gene sequences was prepared with serial analysis of ribosomal sequence tags (SARST) from a composite of contaminated and uncontaminated soils. By designing hybridization probes specific to the 100 most abundant ribosomal sequence tags (RSTs) in the composite library, the RST array was designed to be habitat-specific and predicted to monitor the most abundant polymerase chain reaction (PCR)-amplified phylotypes in the individual samples. The sensitivity and specificity of the RST array was tested with a series of pure culture-specific probes and hybridized with labelled soil PCR products to generate hybridization patterns for each soil. Sequencing of prominent bands in denaturing gradient gel electrophoresis (DGGE) fingerprints derived from these soils provided a means by which we successfully confirmed the habitat-specific array design and validated the bulk of the probe signals. Non-metric multidimensional scaling revealed correlations between probe signals and soil physicochemical parameters. Among the strongest correlations to total HCH contamination were probe signals corresponding to unknown Gamma Proteobacteria, potential pollutant-degrading phylotypes, and several organisms with acid-tolerant phenotypes. The strongest correlations to alpha-HCH were probe signals corresponding to the genus Sphingomonas, which contains known HCH degraders. This suggests that the population detected was enriched in situ by HCH contamination and may play a role in HCH degradation. Other environmental parameters were also likely instrumental in shaping community composition in these soils. The results highlight the power of habitat-specific microarrays for comparing complex microbial communities.     

Biodiversity of soft-sediment benthic communities from Italian transitional waters

Aim For conservation purposes, it is important to understand the forces that shape biodiversity in transitional waters (TWs) and to evaluate the effects of small‐scale latitudinal changes. To this end, we analysed data on soft‐sediment macroinvertebrates from nine Italian TWs in order to (1) investigate the structure and distribution of the benthic fauna and their relationships with environmental and geographical variables, and (2) examine species richness and β‐diversity at various spatial scales. Location European Transition Waters Ecoregion 6. Methods Using a data set collected along a 7° latitudinal cline between 45°28′ N and 39°56′ N, we used Spearman’s rank correlation analysis to evaluate the relationships between species richness and both environmental and geographical variables, and linear regression analysis to show the relationships between α‐, β‐ and γ‐diversity. Three measures were used to assess β‐diversity: Whittaker’s β_W, and two similarity indices, namely the Bray‐Curtis similarity index and Δ_s. Using multivariate analyses, we determined the similarity in composition of the benthic community between sites and compared the biotic ordination with abiotic (geographical and environmental) characteristics. Results Two hundred and sixty‐eight species were recorded from 46 sites. Of these, 53.4% were restricted to one TW. Annelida was the dominant taxonomic group, followed by Crustacea and Mollusca. The α‐diversity was highly variable (5–87 species) and was correlated with latitude. The γ‐diversity, measured at the TW scale, was correlated significantly with α‐diversity. The β‐diversity increased with spatial scale and habitat heterogeneity. In the community pattern identified by multivariate analysis, TWs were segregated by latitude and biogeography, and this reflected different climatic conditions. Main conclusions We found that α‐diversity increased when moving from higher to lower latitudes, and that it depended on both regional and local factors. In addition, we detected latitudinal variations in the extent of regional influence on local species richness. The observed distribution pattern of TW faunas depended mostly on climate type. We suggest that the distribution of annelidan species could be used as a proxy for assessing general community patterns for Italian TWs.     

Biodiversity and extracellular enzymatic activity of heterotrophic bacterial communities in Bardawil Lagoon,Egypt

The biodiversity of heterotrophic viable bacteria (209 isolates) in the hypersaline Bardawil Lagoon, Egypt, was studied. Composition and extracellular activities of viable culturable heterotrophic bacteria (VCHB) in the water and in non-colonised and seagrass-colonised sediments of Bardawil Lagoon were determined bimonthly during 1997 and 1998. The average ± SD total Kjeldhal nitrogen was 1.69 ± 0.44 mg l^?1 in water, 335.95 ± 19.22 mg kg^?1 in colonised sediments, and 215.5 ± 16.0 mg kg^?1 in non-colonised sediments. Exoenzymatic bacterial activity (glycosidase) presented a seasonal trend with average values of 1.02 ±0.16 μM cm^?3 min^?1 in colonised sediment samples and was 0.36 ± 0.27 μM cm^?3 min^?1 in non-colonised sediments. Mean of VCHB was 4 017 ± 565 cfu g^?1 and 1 195 ± 242 cfu g^?1 for colonised and non-colonised sediments, respectively. Bacterial isolates from Bardawil Lagoon water and sediments yielded a wide diversity of VCHB: a total of 209 different species, belonging to 13 genera from the water and 12 genera from the sediments.     

Diversity,abundance, and spatial distribution of riverine microbial communities response to effluents from swine farm versus farmhouse restaurant

The 454 pyrosequencing technique was applied to evaluate microbial community composition in sediment and water samples collected from the river receiving effluents from a swine farm and a farmhouse restaurant, respectively. For each sample, 4,600 effective sequences were selected and used to do the bacterial diversity and abundance analysis, respectively. Bacterial phylotype richness in the river sediment sample without effluent input was higher than the other samples, and the river water sample with addition of effluent from the swine farm had the least richness. Effluents from both the swine farm and the farmhouse restaurant have the potential to decrease the bacterial diversity and abundance in the river sediment and water, especially it is more significant in the river sediment. Effect of effluent from the swine farm on riverine bacterial communities was more significant than that from the farmhouse restaurant. Characterization of bacterial community composition in sediments from two tributaries of the downstream river showed that various effluents from the swine farm and the farmhouse restaurant have the similar potential to reduce the natural variability in riverine ecosystems, and contribute to the biotic homogenization in the river sediment.