rRNA‐based analysis to monitor succession of faecal bacterial communities in Holstein calves

Aims: To quantitatively analyse the faecal bacterial communities of Holstein calves and track their succession up to 12 weeks of age. Methods and Results: Faecal samples obtained from four female Holstein calves were analysed by the RNA‐based, sequence‐specific rRNA cleavage method. Twelve scissor probes covering major rumen bacterial groups were used, detecting c. 60–90% of the total 16S rRNAs. At 1 week of age, 16S rRNAs from members of the Bacteroides‐Prevotella group (40·0% of the total 16S rRNAs), Faecalibacterium (21·7%), the Clostridium coccoides–Eubacterium rectale group (16·7%) and the Atopobium cluster (10·9%) were detected at high levels. Throughout the 12‐week period, rRNAs of the Bacteroides‐Prevotella and the Cl. coccoides‐Eu. rectale groups constituted the major fraction of microbiota (c. 50–70% of the total). The relative abundances of the Atopobium cluster, Faecalibacterium, and some probiotic bacteria (such as those of the genera Lactobacillus and Bifidobacterium) decreased as the animal aged. Instead, an uncultivated rumen bacterial group, as well as Ruminococcus flavefaciens and Fibrobacter emerged at the detectable levels (1–2%) in the faeces sampled at a postweaning age. In addition, certain bacterial groups that were not covered by the probe suite increased as the animals aged. Conclusions: Young calves undergo dynamic changes in their intestinal bacterial community during the first 12 weeks of life. As young ruminants undergo metabolic and physiological development in their digestive tracts in the transition from a monogastric to a ruminant animal at an early age, the intestinal bacterial community may reflect such development. Significance and Impact of the Study: The succession of the bacterial communities in the faeces of calves was quantitatively monitored in the present study for the first time. The approach used here was demonstrated to be a useful means for determining the populations of predominant faecal bacterial groups in a variety of calf experiments in response to diet, stress and disease.     

Investigation of the faecal microbiota of kittens: monitoring bacterial succession and effect of diet

Weaning is a stressful process for kittens and is often associated with diarrhoea and the onset of infectious diseases. The gastrointestinal (GI) microbiota plays an essential role in host well-being, including improving homoeostasis. Composition of the GI microbiota of young cats is poorly understood and the impact of diet on the kitten microbiota unknown. The aims of this study were to monitor the faecal microbiota of kittens and determine the effect(s) of diet on its composition. Bacterial succession was monitored in two groups of kittens (at 4 and 6 weeks, and 4 and 9 months of age) fed different foods. Age-related microbial changes revealed significantly different counts of total bacteria, lactic acid bacteria, Desulfovibrionales, Clostridium cluster IX and Bacteroidetes between 4-week- and 9-month-old kittens. Diet-associated differences in the faecal microbiota of the two feeding groups were evident. In general, fluorescence in situ hybridization analysis demonstrated bifidobacteria, Atopobium group, Clostridium cluster XIV and lactic acid bacteria were dominant in kittens. Denaturing gradient gel electrophoresis profiling showed highly complex and diverse faecal microbiotas for kittens, with age- and/or food-related changes seen in relation to species richness and similarity indices. Four-week-old kittens harboured more diverse and variable profiles than those of weaned kittens.     

Integrated Community Profiling Indicates Long-Term Temporal Stability of the Predominant Faecal Microbiota in Captive Cheetahs

Understanding the symbiotic relationship between gut microbes and their animal host requires characterization of the core microbiota across populations and in time. Especially in captive populations of endangered wildlife species such as the cheetah (Acinonyx jubatus), this knowledge is a key element to enhance feeding strategies and reduce gastrointestinal disorders. In order to investigate the temporal stability of the intestinal microbiota in cheetahs under human care, we conducted a longitudinal study over a 3-year period with bimonthly faecal sampling of 5 cheetahs housed in two European zoos. For this purpose, an integrated 16S rRNA DGGE-clone library approach was used in combination with a series of real-time PCR assays. Our findings disclosed a stable faecal microbiota, beyond intestinal community variations that were detected between zoo sample sets or between animals. The core of this microbiota was dominated by members of Clostridium clusters I, XI and XIVa, with mean concentrations ranging from 7.5-9.2 log10 CFU/g faeces and with significant positive correlations between these clusters (P<0.05), and by Lactobacillaceae. Moving window analysis of DGGE profiles revealed 23.3-25.6% change between consecutive samples for four of the cheetahs. The fifth animal in the study suffered from intermediate episodes of vomiting and diarrhea during the monitoring period and exhibited remarkably more change (39.4%). This observation may reflect the temporary impact of perturbations such as the animal’s compromised health, antibiotic administration or a combination thereof, which temporarily altered the relative proportions of Clostridium clusters I and XIVa. In conclusion, this first long-term monitoring study of the faecal microbiota in feline strict carnivores not only reveals a remarkable compositional stability of this ecosystem, but also shows a qualitative and quantitative similarity in a defined set of faecal bacterial lineages across the five animals under study that may typify the core phylogenetic microbiome of cheetahs.     

An in vitro evaluation of the effects of a Yucca schidigera extract and chestnut tannins on composition and metabolic profiles of canine and feline faecal microbiota

The in vitro effect of a Yucca schidigera extract (YSE) and tannins from chestnut wood on composition and metabolic activity of canine and feline faecal microbiota was evaluated. Four treatments were carried out: control diet, chestnut tannins (CT), YSE and CT + YSE. The YSE was added to canine and feline faecal cultures at 0.1 g/l, while CT were added at 0.3 g/l for a 24-h incubation. A total of 130 volatile compounds were detected by means of headspace-solid phase microextraction gas-chromatography/mass spectrometry analyses. Several changes in the metabolite profiles of fermentation fluids were found, including a decrease of alcohols (?19%) and esters (?42%) in feline and canine inoculum, respectively, which was due to the antibacterial properties of tannins. In canine inoculum, after 6 h, YSE + CT caused lower cadaverine concentrations (?37%), while ammonia (?4%) and quinolone (?27%) were reduced by addition of CT. After 24 h, the presence of CT resulted in a decrease of sulphur compounds, such as dimethyl sulphide (?69%) and dimethyl disulphide (?20%). In feline faecal cultures, after 6 h, CT lowered the amount of indole (?48%), whereas YSE tended to decrease trimethylamine levels (?16%). Both in canine and feline inoculum, addition of CT and, to a minor extent, YSE affected volatile fatty acids patterns. In canine faecal cultures, CT exerted a marginal inhibitory effect on Escherichia coli population (?0.45 log 10 numbers of DNA copies/ml), while enterococci were increased (+2.06 log 10 numbers of DNA copies/ml) by YSE. The results from the present study show that YSE and tannins from chestnut wood exert different effects on the composition and metabolism of canine and feline faecal microbiota. In particular, the supplementation of YSE and tannins to diets for dogs and cats may be beneficial due to the reduction of the presence of some potentially toxic volatile metabolites in the animals’ intestine.     

Captive environment influences the composition and diversity of fecal microbiota in Indo-Pacific bottlenose dolphins,Tursiops aduncus

Captive environments impact the microbiota of captive animals; however, the comparison of microbiota between wild and captive dolphins has been poorly investigated. To explore the impact of a captive environment, we characterized the fecal microbiota of nine wild and four captive Indo-Pacific bottlenose dolphins, Tursiops aduncus, using a next-generation sequencing and revealed differences in the fecal microbiota between the analyzed groups. Statistical differences in abundances of the phyla Firmicutes and Proteobacteria were found between the wild and captive dolphins. Thirty-six genera (22.9% of the total genera detected in all dolphins) were shared between the groups, whereas 79 (50.3%) and 42 (26.8%) genera were found only in the wild or captive dolphins, respectively. Several pathogenic bacterial genera, including Morganella and Mycoplasma, were detected only in the captive dolphins, and the genus Lactobacillus was found only in the wild dolphins. LefSe and SIMPER analyses revealed that the genus Clostridium sensu stricto 1 was significantly more abundant in the captive dolphins than in the wild ones and contributed the most to the dissimilarity of fecal microbiota between the groups. Our results indicate that the captive environment impacts the fecal microbiota of dolphins and reinforces the importance of monitoring potentially pathogenic bacteria in captivity.     

In vitro measurement of the impact of human milk oligosaccharides on the faecal microbiota of weaned formula-fed infants compared to a mixture of prebiotic fructooligosaccharides and galactooligosaccharides

Aims: To investigate the impact of human milk oligosaccharides (HMOs) from a single donor (SO), HMOs from multiple donors (PO), a fructooligosaccharides and galactooligosaccharides mixture (FG) on the composition of a batch culture inoculated with faecal microbiota from formula‐fed infants. Methods and Results: Three substrates were compared using 24‐h pH‐controlled anaerobic batch cultures inoculated with infant faecal slurries. Changes in bacterial populations, short‐chain fatty acids (SCFA) production and bacterial 16S rRNA gene profiles were determined. All three substrates significantly increased numbers of bifidobacteria, bacteroides and those aligning with the clostridial cluster XIVa. Neither the FG nor the HMOs substrates supported the growth of the Clostridium perfringens–histolyticum group. SCFA production corresponded to changes observed in bacterial populations. Denaturing gradient gel electrophoresis fingerprint analysis showed a distinct profile of faecal bacteria present in each infant. Conclusions: HMOs modulated infant faecal culture composition in a similar manner to the prebiotic mixture FG in vitro. Significance and Impact of the Study: This is the first demonstration of the impact of pure HMOs on the mixed culture of infant faecal bacteria. HMOs induced the growth of several saccharolytic bacterial groups and may thus play a role in the health‐promoting attributes of human breast milk and have an extended significance in infant diet during/after weaning.     

Isolation of faecal coliform bacteria from the American alligator (Alligator mississippiensis)

Aims: To determine whether American alligators (Alligator mississippiensis) are an unrecognized poikilothermic source of faecal coliform and/or potential pathogenic bacteria in South Carolina’s coastal waters. Methods and Results: Bacteria from the cloaca of American alligators, as well as bacteria from surface water samples from their aquatic habitat, were isolated and identified. The predominant enteric bacteria identified from alligator samples using biochemical tests included Aeromonas hydrophila, Citrobacter braakii, Edwardsiella tarda, Escherichia coli, Enterobacter cloacae, Plesiomonas shigelloides and putative Salmonella, and these were similar to bacteria isolated from the surface waters in which the alligators inhabited. Based on most‐probable‐number enumeration estimates from captive alligator faeces, faecal coliform bacteria numbered 8·0 × 10⁹ g^?1 (wet weight) of alligator faecal material, a much higher concentration than many other documented endothermic animal sources. Conclusions: A prevalence of enteric bacteria, both faecal coliforms and potential pathogens, was observed in American alligators. The high faecal coliform bacterial density of alligator faeces may suggest that alligators are a potential source of bacterial contamination in South Carolina coastal waters. Significance and Impact of the Study: These findings help to increase our understanding of faecal coliform and potential pathogenic bacteria from poikilothermic reptilian sources, as there is the potential for these sources to raise bacterial water quality levels above regulatory thresholds.     

Initial butyrate producers during infant gut microbiota development are endospore formers

The acquisition of the infant gut microbiota is key to establishing a host-microbiota symbiosis. Microbially produced metabolites tightly interact with the immune system, and the fermentation-derived short-chain fatty acid butyrate is considered an important mediator linked to chronic diseases later in life. The intestinal butyrate-forming bacterial population is taxonomically and functionally diverse and includes endospore formers with high transmission potential. Succession, and contribution of butyrate-producing taxa during infant gut microbiota development have been little investigated. We determined the abundance of major butyrate-forming groups and fermentation metabolites in faeces, isolated, cultivated and characterized the heat-resistant cell population, which included endospores, and compared butyrate formation efficiency of representative taxa in batch cultures. The endospore community contributed about 0.001% to total cells, and was mainly composed of the pioneer butyrate-producing Clostridium sensu stricto. We observed an increase in abundance of Faecalibacterium prausnitzii, butyrate-producing Lachnospiraceae and faecal butyrate levels with age that is likely explained by higher butyrate production capacity of contributing taxa compared with Clostridium sensu stricto. Our data suggest that a successional arrangement and an overall increase in abundance of butyrate forming populations occur during the first year of life, which is associated with an increase of intestinal butyrate formation capacity.     

Distribution of integron-associated trimethoprim–sulfamethoxazole resistance determinants among Escherichia coli from humans and food-producing animals

Aims: To compare the distribution of integrons and trimethoprim–sulfamethoxazole resistance genes among Escherichia coli isolates from humans and food‐producing animals. Methods and Results: A collection of 174 multidrug‐resistant E. coli isolates obtained from faecal samples of food‐producing animals (n = 64) and humans (n = 59), and patients with urinary tract infections (n = 51) in Hong Kong during 2002–2004 were studied. The strains were analysed for their phylogenetic groups, the presence of sul genes (sul1 and sul2), integrons (intl1 and intl2) and class 1 integron‐associated dfr cassette genes by PCR, restriction enzyme analysis and sequencing. Integrons were identified in 110 (63·2%) isolates. The prevalence of integrons was significantly different according to the specimen sources (animal faecal 84·4%, human faecal 67·8% and human urinary 31·4%) and phylogenetic groups (B1 80·8%, A 77·6%, D 54·1% and B2 11·5%). Faecal isolates (both human and animal) are more likely to belong to group A and B1. In contrast, most urinary isolates were either groups B2 and D. Among dfr containing isolates, dfrA1 and dfrA12 were almost exclusively found in strains of phylogenetic groups A and B1; and were present in animal and human faecal isolates. In contrast, dfrA17 was found in both faecal and urinary isolates and comprised strains from all phylogenetic groups. The sul1 and sul2 genes were equally prevalent among the isolates irrespective of the specimen source and phylogenetic group status. Pulsed‐field gel electrophoresis analysis of isolates with identical cassette genes showed that they were genetically diverse. Conclusions: More animal faecal isolates carry class 1 integrons than human faecal and human urinary isolates, and the distribution of phylogenetic groups is common across animal and human faecal isolates but different from human urinary isolates. Significance and Impact of the Study: Commensal isolates from food‐producing animals are an important reservoir for integrons carrying antibiotic resistance genes.     

Green kiwifruit modulates the colonic microbiota in growing pigs

Aims: To investigate whether green kiwifruit modulates the composition of colonic microbiota in growing pigs. Methods and Results: Thirty‐two pigs were fed the control diet or one of the three test diets containing either cellulose, freeze‐dried kiwifruit or kiwifruit fibre as the sole fibre source for 14‐day study. A Ward’s dendrogram of similarity cluster analysis on PCR‐DGGE gels revealed that inclusion of freeze‐dried kiwifruit and kiwifruit fibre into diets altered the bacterial community, indicating the presence of two distinct clusters. Quantification of different bacterial groups by qPCR demonstrated that pigs fed the freeze‐dried kiwifruit or kiwifruit fibre diets had a significantly higher number (P < 0·05) of total bacteria and Bacteroides group and a lower number of Enterobacteria and Escherichia coli group, as well as a greater ratio of Lactobacillus to Enterobacteria when compared to pigs fed the control or cellulose diets. Conclusions: Green kiwifruit, mainly because of fibre, modulated the colonic microbiota, leading to an improved intestinal environment in growing pigs. Significance and Impact of the Study: This is the first report regarding the effect of green kiwifruit on gut microbiota using the in vivo pig model. These results provide the first evidence of interaction between green kiwifruit and colonic microbiota.     

Investigation of the impact of feeding Lactobacillus plantarum CRL 1815 encapsulated in microbially derived polymers on the rat faecal microbiota

Aims

The aim of this study was to evaluate the impact of the administration of microencapsulated Lactobacillus plantarum CRL 1815 with two combinations of microbially derived polysaccharides, xanthan : gellan gum (1%:0·75%) and jamilan : gellan gum (1%:1%), on the rat faecal microbiota.

Methods and Results

A 10‐day feeding study was performed for each polymer combination in groups of 16 rats fed either with placebo capsules, free or encapsulated Lact. plantarum or water. The composition of the faecal microbiota was analysed by fluorescence in situ hybridization and temporal temperature gradient gel electrophoresis. Degradation of placebo capsules was detected, with increased levels of polysaccharide‐degrading bacteria. Xanthan : gellan gum capsules were shown to reduce the Bifidobacterium population and increase the Clostridium histolyticum group levels, but not jamilan : gellan gum capsules. Only after administration of jamilan : gellan gum‐probiotic capsules was detected a significant increase in Lactobacillus‐Enterococcus group levels compared to controls (capsules and probiotic) as well as two bands were identified as Lact. plantarum in two profiles of ileum samples.

Conclusions

Exopolysaccharides constitute an interesting approach for colon‐targeted delivery of probiotics, where jamilan : gellan gum capsules present better biocompatibility and promising results as a probiotic carrier.

Significance and Impact of Study

This study introduces and highlights the importance of biological compatibility in the encapsulating material election, as they can modulate the gut microbiota by themselves, and the use of bacterial exopolysaccharides as a powerful source of new targeted‐delivery coating material.     

Escherichia coli and enterococci are sensitive and reliable indicators for human,livestock and wildlife faecal pollution in alpine mountainous water resources

Aims: This study evaluated the applicability of standard faecal indicator bacteria (SFIB) for alpine mountainous water resources monitoring. Methods and Results: Escherichia coli, enterococci (ENTC) and Clostridium perfringens were investigated by standard or frequently applied phenotypic and genotypic methods in a broad range of animal and human faecal sources in a large alpine mountainous area. Clostridium perfringens occurred only in human, livestock and carnivorous source groups in relevant average concentrations (log 4·7–7·0 CFU g^?1) but not in herbivorous wildlife sources. Escherichia coli proved to be distributed in all faecal source groups with remarkably balanced average concentrations (log 7·0–8·4 CFU g^?1). Except for single faecal samples from the cattle source group, prevalence rates for ENTC source groups were generally >87% with average concentrations of log 5·3–7·7 CFU g^?1. To test the faecal indication capacity in the environment, faecal prevalence data were comparatively analysed with results from the concurrently performed multi‐parametric microbial source tracking effort on karst spring water quality from the investigated alpine mountainous catchment ( Reischer et al. 2008 ; Environ Microbiol 10:2598–2608). Conclusion: Escherichia coli and enterococci are reliable faecal indicators for alpine mountainous water resources monitoring, although E. coli is the more sensitive one. Clostridium perfringens did not prove to be an indicator of general faecal pollution but is suggested a conservative microbial source tracking marker for anthropogenic faecal influence. Significance and Impact of the Study: Applicability of SFIB is currently hotly debated. This is the first study providing comprehensive information on the applicability of SFIB at alpine mountainous habitats.     

Faecal Microbiota of Cats with Insulin-Treated Diabetes Mellitus

Microorganisms within the gastrointestinal tract significantly influence metabolic processes within their mammalian host, and recently several groups have sought to characterise the gastrointestinal microbiota of individuals affected by metabolic disease. Differences in the composition of the gastrointestinal microbiota have been reported in mouse models of type 2 diabetes mellitus, as well as in human patients. Diabetes mellitus in cats has many similarities to type 2 diabetes in humans. No studies of the gastrointestinal microbiota of diabetic cats have been previously published. The objectives of this study were to compare the composition of the faecal microbiota of diabetic and non-diabetic cats, and secondarily to determine if host signalment and dietary factors influence the composition of the faecal microbiota in cats. Faecal samples were collected from insulin-treated diabetic and non-diabetic cats, and Illumina sequencing of the 16S rRNA gene and quantitative PCR were performed on each sample. ANOSIM based on the unweighted UniFrac distance metric identified no difference in the composition of the faecal microbiota between diabetic and non-diabetic cats, and no significant differences in the proportions of dominant bacteria by phylum, class, order, family or genus as determined by 16S rRNA gene sequencing were identified between diabetic and non-diabetic cats. qPCR identified a decrease in Faecalibacterium spp. in cats aged over ten years. Cat breed or gender, dietary carbohydrate, protein or fat content, and dietary formulation (wet versus dry food) did not affect the composition of the faecal microbiota. In conclusion, the composition of the faecal microbiota was not altered by the presence of diabetes mellitus in cats. Additional studies that compare the functional products of the microbiota in diabetic and non-diabetic cats are warranted to further investigate the potential impact of the gastrointestinal microbiota on metabolic diseases such as diabetes mellitus in cats.     

体外法探究猪空肠和回肠黏膜微生物对低聚半乳糖和低聚甘露糖的发酵特性

【背景】小肠黏膜微生物是肠道菌群的重要组成部分,大量研究表明日粮添加低聚半乳糖（galacto-oligosaccharides,GOS）和低聚甘露糖（manno-oligosaccharides,MOS）能够调控猪的大肠菌群结构,但关于其调控小肠黏膜微生物的研究较少。【目的】通过体外发酵法探究猪空肠黏膜和回肠黏膜微生物发酵GOS和MOS的规律。【方法】以生长猪的空肠黏膜微生物和回肠黏膜微生物作为接种物,以GOS和MOS作为底物进行厌氧发酵,在发酵0、6、12、24 h时采样测定总菌数量、pH、氨态氮（ammonia nitrogen,NH₃-N）、菌体蛋白（microbial crude protein,MCP）和有机酸,在24 h收集微生物提取DNA进行细菌定量分析。【结果】在24 h时,回肠黏膜组的NH₃-N浓度显著低于空肠黏膜组,而MCP浓度显著高于空肠黏膜组（P<0.05）。在发酵的前6 h各组pH无明显变化,有机酸积累较少。在12 h时,MOS组的乳酸、乙酸、丁酸和总短链脂肪酸产量显著高于GOS组（P<0.05）,此时只有回肠黏膜组有少量丙酸产生。在24 h时,MOS回肠黏膜组乳酸产量最高而pH值最低（P<0.05）。相较于MOS组,GOS组显著提高了丙酸的产量（P<0.05）。相较于GOS组,MOS组显著提高了乙酸的产量,在空肠黏膜组中显著提高了丁酸和总短链脂肪酸的产量（P<0.05）。定量结果表明,在24 h时,各处理组的厚壁菌门数量都接近总菌数量,属于优势菌门。相较于MOS组,GOS组显著提高了拟杆菌门、链球菌属、韦荣氏球菌属和普拉梭菌细菌的数量,提高了空肠黏膜组中Clostridium cluster IV和回肠黏膜组中Clostridium cluster XIVa的数量（P<0.05）。相较于GOS组,MOS组显著提高了大肠杆菌和乳酸杆菌属的数量,提高了回肠黏膜组中罗氏菌属的数量（P<0.05）。【结论】猪小肠黏膜微生物对GOS和MOS具有不同的发酵模式,主要表现在有机酸的产生和促进细菌的增殖方面。GOS具有产丙酸优势,提高了拟杆菌门和韦荣氏球菌属的数量;MOS促进了乙酸的产生,提高了大肠杆菌和乳酸杆菌的数量。     

Role of the probiotic strain Lactobacillus paracasei LMGP22043 carried by artichokes in influencing faecal bacteria and biochemical parameters in human subjects

Aims: To evaluate the positive influence of the probiotic strain Lactobacillus paracasei LMGP22043 carried by artichokes into the human gut with special reference to faecal bacterial balance, short‐chain fatty acid concentrations and enzyme activities in a randomized, double‐blind human trial in comparison with probiotic‐free artichokes (control). Methods: Twenty subjects were randomized into two groups, which consumed daily 180 g of the artichoke product (probiotic or control) during two 15‐day study periods (periods 1 and 2) separated by a 15‐day washout in a crossover manner. Faecal samples were subjected to microbiological and biochemical analyses, and a strain‐specific PCR was performed to monitor the probiotic strain. Results: The probiotic strain, transported by the vegetable matrix, transiently colonized the gut of 17/20 subjects (median 6·87 log CFU g^?1 faeces), antagonized Escherichia coli and Clostridium spp. and increased the genetic diversity of lactic population based on REP‐PCR profiles, mainly after period 1. Conclusions: The probiotic L. paracasei LMGP22043 successfully colonized the human gut and positively influenced faecal bacteria and biochemical parameters. Significance and Impact of the Study: The association of the probiotic L. paracasei with a food carrier rich in fibre can represent a new strategy for favouring a daily supply of probiotics and attracting more consumers to vegetable food fortified with probiotic strains.     

Indicator bacteria in freshwater and marine molluscs

The freshwater mussel Anodonta cygnea and four marine shellfish (mussels, Mytilus edulis; cockles, Cerastoderma edule; clams, Mya arenaria; Scrobicularia plana) from a total of six sites were surveyed for Escherichia coli, Clostridium perfringens, faecal streptococci, 25 and 37 °C coliforms, 25 °C and 37 °C total viable numbers and fluorescent pseudomonads. The A. cygnea from an urban lake contained greater numbers of the faecal indicator bacteria than animals from a rural lake. There were also differences in the other bacterial counts and these were discussed with respect to bacterial parameter and animal characteristics. When freshwater mussels were transferred from the city site to the rural site for 24 h the load of faecal indicator bacteria was eliminated or significantly reduced. Other bacterial types took longer to become stabilised. Loss of indicator bacteria from Anodonta was also demonstrated using cleansing in the laboratory. Very high bacterial numbers were found in some marine molluscs notably Scrobicularia plana and most shellfish contained significant numbers of the three faecal indicator bacteria at every sampling occasion. The relationship between bacterial types was discussed and it was concluded that in both freshwater and marine animals the bacterial numbers were determined more by sampling site than by species of shellfish.     

Microbial fingerprinting detects unique bacterial communities in the faecal microbiota of rats with experimentally-induced colitis

An abnormal composition of the gut microbiota is believed to be associated with the pathogenesis of inflammatory bowel disease (IBD). We utilized terminal restriction fragment length polymorphism (T-RFLP) analysis to quantify faecal bacterial communities from rats with experimental colitis. Male Sprague Dawley rats (n=10/group) ingested 2% dextran sulfate sodium (DSS) or water for up to 7 days. Rats were killed and colonic tissues collected for histological analysis. Damage severity score in the distal colon was significantly greater (P<0.001) following DSS consumption compared to controls. T-RFLP faecal bacterial profiles generated with either MspI or CfoI revealed a significant difference (P<0.001) in community composition between healthy and colitic rats, with bacterial composition in healthy rats more variable than in rats with colitis. Operational taxonomic units (OTU: taxonomically related groups of bacteria) associated with either the healthy or colitic state were identified. OTU (116, 226, 360, and 948; CfoI) and (118 and 188; MspI) were strongly associated with untreated healthy rats, while OTU (94, 98, 174, and 384; CfoI) and (94 and 914; MspI) were predominantly associated with DSS-treated colitic rats. Phylogenetic OTU assignment suggested that Bacteroidales and Lactobacillus sp. were predominantly associated with the colitic and healthy rats, respectively. These results show that faecal bacterial profiling is a rapid, sensitive and non-invasive tool for detecting and identifying changes in gut microbiota associated with colitis. Restoring microbial homeostasis by targeting colitis-associated OTU through specific microbiological interventions could form the basis of novel therapeutic strategies for IBD.     

Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats

This study evaluated the fecal microbiota of 12 healthy pet dogs and 12 pet cats using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing. A total of 120,406 pyrosequencing reads for bacteria (mean 5017) and 5359 sequences (one pool each for dogs and cats) for fungi were analyzed. Additionally, group-specific 16S rRNA gene clone libraries for Bifidobacterium spp. and lactic acid-producing bacteria (LAB) were constructed. The most abundant bacterial phylum was Firmicutes, followed by Bacteroidetes in dogs and Actinobacteria in cats. The most prevalent bacterial class in dogs and cats was Clostridia, dominated by the genera Clostridium (clusters XIVa and XI) and Ruminococcus. At the genus level, 85 operational taxonomic units (OTUs) were identified in dogs and 113 OTUs in cats. Seventeen LAB and eight Bifidobacterium spp. were detected in canine feces. Ascomycota was the only fungal phylum detected in cats, while Ascomycota, Basidiomycota, Glomeromycota, and Zygomycota were identified in dogs. Nacaseomyces was the most abundant fungal genus in dogs; Saccharomyces and Aspergillus were predominant in cats. At the genus level, 33 different fungal OTUs were observed in dogs and 17 OTUs in cats. In conclusion, this study revealed a highly diverse bacterial and fungal microbiota in canine and feline feces.     

Dynamics of bacterial community development in the reef coral <Emphasis Type="Italic">Acropora muricata</Emphasis> following experimental antibiotic treatment

Development of the bacterial community associated with the coral Acropora muricata (=formosa) was monitored using 16S rRNA gene-based techniques and abundance counts over time following experimental modification of the existing microbial community using the antibiotic ciprofloxacin. Abundance of bacteria was reduced >99% by the treatment, resulting in significant changes in bacterial community structure. Following redeployment to their natural environment, some settlement and re-growth of bacteria took place within a few hours, including ribosomal types that were not present, or in low abundance, in the natural microbiota. However, complete recovery of the bacterial community required longer than 96 h, which indicates a relatively slow settlement and growth of bacteria from the water column and suggests that turnover of the natural community is similarly slow. The early developing community was dominated by antibiotic-resistant bacteria from the natural microbiota that survived the treatment and proliferated in the absence of natural competitors, but also included some non-resident ribotypes colonizing from the water column. Almost, all these opportunists were significantly reduced or eliminated within 96 h after treatment, demonstrating a high resilience in the natural bacterial community. Potential pathogens, including a Clostridium sp., inhabited the coral at low abundances, only becoming prevalent when the natural microbiota was disturbed by the treatment. The healthy coral-associated microbiota appears to be strongly controlled by microbial interactions.     

Microbiota profile in feces of breast- and formula-fed newborns by using fluorescence in situ hybridization (FISH)

The development of the gut is controlled and modulated by different interacting mechanisms such as, genetic endowment, intrinsic biological regulatory functions, environment influences and last but no least, the diet influence. Considered together with other endogenous and exogenous factors the type of feeding may interfere greatly in the regulation of the intestinal microbiota. During the last years molecular methods offer a complementarity to the classic culture-based knowledge. FISH has been applied for molecular evaluation of the microbiota in newborns delivered by vaginal delivery. Eleven probes/probe combinations for specific groups of faecal bacteria were used to determine the bacterial composition in faecal samples of newborns infants under different types of feeding. Breast-fed infants harbor a fecal microbiota by more than two times increased in numbers of Bifidobacterium cells when compared to formula-fed infants. After formula-feeding, Atopobium was found in significant counts and the numbers of Bifidobacterium dropped followed by increasing numbers in Bacteroides population. Moreover, under formula feeding the infants microbiota was more diverse.