Design and evaluation of group-specific oligonucleotide probes for quantitative analysis of intestinal ecosystems: their application to assessment of equine colonic microflora

Fibrobacter sp. HC4, a newly isolated strain, demonstrates a high cellulolytic activity as revealed by enzymatic measurements and in vitro assay

Despite their low quantity and abundance, the cellulolytic bacteria that inhabit the equine large intestine are vital to their host, as they enable the crucial use of forage-based diets. Fibrobacter succinogenes is one of the most important intestinal cellulolytic bacteria. In this study, Fibrobacter sp. HC4, one cellulolytic strain newly isolated from the horse cecum, was characterized for its ability to utilize plant cell wall fibers. Fibrobacter sp. HC4 consumed only cellulose, cellobiose, and glucose and produced succinate and acetate in equal amounts. Among genes coding for CAZymes, 26% of the detected glycoside hydrolases (GHs) were involved in cellulolysis. These cellulases belong to the GH5, GH8, GH9, GH44, GH45, and GH51 families. Both carboxymethyl cellulase and xylanase activities of Fibrobacter sp. HC4 were detected using the Congo red method and were higher than those of F. succinogenes S85, the type strain. The in vitro addition of Fibrobacter sp. HC4 to a fecal microbial ecosystem of horses with large intestinal acidosis significantly enhanced fibrolytic activity as measured by the increase in gas and volatile fatty acids production during the first 48 h. According to this, the pH decreased and the disappearance of dry matter increased at a faster rate with Fibrobacter sp. HC4. Our data suggest a high specialization of the new strain in cellulose degradation. Such a strain could be of interest for future exploitation of its probiotic potential, which needs to be further determined by in vivo studies.IMPORTANCECellulose is the most abundant of plant cell wall fiber and can only be degraded by the large intestine microbiota, resulting in the production of volatile fatty acids that are essential for the host nutrition and health. Consequently, cellulolytic bacteria are of major importance to herbivores. However, these bacteria are challenged by various factors, such as high starch diets, which acidify the ecosystem and reduce their numbers and activity. This can lead to an imbalance in the gut microbiota and digestive problems such as colic, a major cause of mortality in horses. In this work, we characterized a newly isolated cellulolytic strain, Fibrobacter sp. HC4, from the equine intestinal microbiota. Due to its high cellulolytic capacity, reintroduction of this strain into an equine fecal ecosystem stimulates hay fermentation in vitro. Isolating and describing cellulolytic bacteria is a prerequisite for using them as probiotics to restore intestinal balance.

Cellulolytic bacteria in the large intestine of mammals

The utilization of dietary cellulose by resident bacteria in the large intestine of mammals, both herbivores and omnivores (including humans), has been a subject of interest since the nineteenth century. Cellulolytic bacteria are key participants in this breakdown process of cellulose, which is otherwise indigestible by the host. They critically contribute to host nutrition and health through the production of short-chain fatty acids, in addition to maintaining the balance of intestinal microbiota. Despite this key role, cellulolytic bacteria have not been well studied. In this review, we first retrace the history of the discovery of cellulolytic bacteria in the large intestine. We then focus on the current knowledge of cellulolytic bacteria isolated from the large intestine of various animal species and humans and discuss the methods used for isolating these bacteria. Moreover, we summarize the enzymes and the mechanisms involved in cellulose degradation. Finally, we present the contribution of these bacteria to the host.

Necrotizing Gingivitis: Microbial Diversity and Quantification of Protein Secretion in Necrotizing Gingivitis

Necrotizing gingivitis (NG) is a necrotizing periodontal disease that differs from chronic gingivitis (CG). To date, both the microbiological causes and the involved host cytokine response of NG still remain unclear. Here, we investigated corresponding interdental plaque and serum samples from two groups of Chinese patients with CG (n = 21) or NG (n = 21). The microbiota were studied by 16S rRNA Illumina MiSeq sequencing of the microbial metagenome and by assessing quantitatively the abundance of the phylum Bacteroidetes, the genus Prevotella and the species T. forsythia, P. endodontalis, and P. gingivalis using fluorescence in situ hybridization (FISH). With respect to the associated host response, the levels of 30 inflammatory mediators were quantified by multiplex immunoassay analysis. Differential microbial abundance analysis of the two disease groups revealed at the phylum level that Proteobacteria accounted for 67% of the differentially abundant organisms, followed by organisms of Firmicutes (21%) and Actinobacteria (9%). At the species level, significant differences in abundance were seen for 75 species of which 58 species were significantly more abundant in CG patients. Notably, the FISH analysis revealed that Bacteroidetes was the most prevalent phylum in NG. The multiplex cytokine assay showed significant quantitative differences between the disease groups for eight analytes (GM–CSF, G–CSF, IFN–α, IL–4, IL–13, TNF–α, MIG, and HGF). The G–CSF was found to be the most significantly increased inflammatory protein marker in NG. The next-generation sequencing (NGS) data supported the understanding of NG as a multi-microbial infection with distinct differences to CG in regard to the microbial composition.

What Would Be Good for All Veterinarians to Know About Equine Nutrition

Nutrition and management have enabling and supporting roles to play in the health, welfare, and performance of equines. Poor or inappropriate nutrition may therefore impose limits on an animal's ability to perform and adversely affect health and welfare. Understanding the gastrointestinal tract from a nutrition perspective can help to reduce the risk of certain clinical problems. This article outlines key factors with respect to the equine digestive tract and discusses relevant aspects of ration formation. Forage is highlighted, because inappropriate forage provision is one of the key limitations in many horse diets.

Idiopathic peritonitis in horses: a retrospective study of 130 cases in Sweden (2002-2017)

BACKGROUND

Peritonitis in horses is historically associated with prolonged treatment regimens of broad-spectrum antimicrobials and a guarded prognosis for survival. The condition is most often seen as a secondary complication to traumatic injuries involving the abdominal cavity, rupture of bowel or abdominal surgery. However, cases of idiopathic peritonitis with no such underlying cause have been described. In Sweden idiopathic peritonitis is commonly identified and, in contrast to peritonitis secondary to traumatic incidents, affected horses appear to respond well to medical treatment. The objectives of this study were to describe clinical signs, laboratory findings, bacterial culture results, treatment regimens and survival rates for horses diagnosed with idiopathic peritonitis.

RESULTS

Medical records were obtained from horses diagnosed with peritonitis without identifiable cause. Diagnosis was based on macroscopically abnormal peritoneal fluid, with an elevated nucleated cell count (> 10 × 10⁹ cells/L) or total protein (> 25 g/L). A total of 130 horses were included, presenting with pyrexia (83%), lethargy (80%), anorexia (68%) and abdominal pain (51%). Microbial cultures were performed in 84% of the cases of which 41% were positive. The most commonly recovered bacteria were Actinobacillus spp., cultured from 21% of the submitted samples. All horses received antimicrobial therapy and many responded to treatment with penicillin alone. Survival until discharge was 94%.

CONCLUSIONS

Idiopathic peritonitis is a disease that should be considered in horses presented with fever, signs of colic and lethargy. Medical treatment of idiopathic peritonitis is often successful and in Sweden most cases appear to respond well to treatment with penicillin as the sole antimicrobial.

Equine Fecal Microbiota Changes Associated With Anthelmintic Administration

The gastrointestinal microbiota (GIM) plays an essential role in maintaining intestinal homeostasis with disruptions having profound effects on the wellbeing of the host animal. Parasitic infection is a long-standing issue for the equine industry, and the use of anthelmintic drugs for parasite control has long been standard practice. The impact of anthelmintic treatment on the GIM in healthy horses is not well known. This study evaluated the hypothesis that anthelmintic administration will alter the equine fecal microbiota in horses without an observed helminth infection. Ten horses were treated with a single dose of QUEST PLUS (active ingredients: Moxidectin and Praziquantel) (Zoetis), and fecal samples were collected before and after treatment. Amplicon sequencing data were quality filtered, processed, and analyzed using QIIME2. Anthelmintic treatment corresponded with a small but significant decrease in alpha diversity (P-value < .05). Analysis of taxonomic abundances before and after treatment with DESeq2 identified 21 features that were significantly different after treatment (P_adj-value < .05). Differences in beta diversity associated with treatment were not significant and potentially suggest factors unique to the individual may play an essential role in the specific responses observed. Overall, the present study does not indicate a broad, large-scale impact on the GIM after anthelmintic treatment. The results do, however, suggest the potential of individualized responses that are based instead on host factors. Identification of these factors and investigation of their impact on the host/microbiota relationship will contribute significantly to our understanding of the role of the microbiome in horse health.

Host selectively contributes to shaping intestinal microbiota of carnivorous and omnivorous fish

Fish production is increasingly important to global food security. A major factor in maintaining health, productivity and welfare of farmed fish is the establishment and promotion of a stable and beneficial intestinal microbiota. Understanding the effects of factors such as host and environment on gut microbial community structure is essential for developing strategies for stimulating the establishment of a health-promoting gut-microbiota. We compared intestinal microbiota of common carp and rainbow trout, two fish with different dietary habits, sourced from various farm locations. There were distinct differences in the gut microbiota of carp and trout intestine. The microbiota of carp was dominated by Fusobacteriia and Gammaproteobacteria, while the trout microbiota consisted predominantly of Mollicutes and Betaproteobacteria. The majority of bacterial sequences clustered into a relatively low number of operational taxonomic units (OTUs) revealing a comparatively simple microbiota, with Cetobacterium, Aeromonas and Mycoplasma being highly abundant. Within each species, fish from different facilities were found to have markedly similar predominant bacterial populations despite distinctly different rearing environments, demonstrating intra-species uniformity and significant influence of host selectivity. This study demonstrates that in fish the host species imparts substantial impact in shaping the community structure of the intestinal microbiota.

Composition and diversity of mucosa-associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences

Mucosa-associated microbial populations of the gastrointestinal tract are in intimate contact with the outer mucus layer. This proximity offers these populations a higher potential, than lumenal microbiota, in exerting effects on the host. Functional characteristics of the microbiota and influences of host-physiology shape the composition and activity of the mucosa-associated bacterial community. We have shown previously that inclusion of an artificial sweetener, SUCRAM, included in the diet of weaning piglets modulates the composition of lumenal-residing gut microbiota and reduces weaning-related gastrointestinal disorders. In this study, using Illumina sequencing we characterised the mucosa-associated microbiota along the length of the intestine of piglets, and determined the effect of SUCRAM supplementation on mucosa-associated populations. There were clear distinctions in the composition of mucosa-associated microbiota, between small and large intestine, concordant with differences in regional oxygen distribution and nutrient provision by the host. There were significant differences in the composition of mucosa-associated compared with lumenal microbiota in pig caecum. Dietary supplementation with SUCRAM affected mucosa-associated bacterial community structure along the length of the intestinal tract. Most notably, there was a substantial reduction in predominant Campylobacter populations proposing that SUCRAM supplementation of swine diet has potential for reducing meat contamination and promoting food safety.

Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus

Disruption in stable establishment of commensal gut microbiota by early weaning is an important factor in susceptibility of young animals to enteric disorders. The artificial sweetener SUCRAM [consisting of neohesperidin dihydrochalcone (NHDC) and saccharin] included in piglets' feed reduces incidence of enteric disease. Pyrosequencing of pig caecal 16S rRNA gene amplicons identified 25 major families encompassing seven bacterial classes with Bacteroidia, Clostridia and Bacilli dominating the microbiota. There were significant shifts in microbial composition in pigs maintained on a diet containing SUCRAM, establishing SUCRAM as a major influence driving bacterial community dynamics. The most notable change was a significant increase of Lactobacillaceae population abundance, almost entirely due to a single phylotype, designated Lactobacillus 4228. The sweetener-induced increase in Lactobacillaceae was observed in two different breeds of pigs signifying a general effect. We isolated Lactobacillus 4228, sequenced its genome and found it to be related to Lactobacillus amylovorus. In vitro analyses of Lactobacillus 4228 growth characteristics showed that presence of NHDC significantly reduces the lag phase of growth and enhances expression of specific sugar transporters, independently of NHDC metabolism. This study suggests that sensing of NHDC by a bacterial plasma membrane receptor underlies sweetener-induced growth of a health promoting gut bacterium.

Temporal changes in the bacterial community of animal feces and their correlation with stable fly oviposition, larval development, and adult fitness

Stable flies are blood-feeding insects with a great negative impact on animals world wide. Larvae develop primarily in animal manure and bacteria are essential for larval development; however, the principle of this dependence is not understood. We hypothesized that as the microbial community of animal manure changes over time, it plays an important role in stable fly fitness. Two-choice bioassays were conducted using 2 week old horse manure (control) and aging horse manure (fresh to 5 week old) to evaluate the effect of manure age on stable fly oviposition. Our data showed that fresh feces did not stimulate oviposition and that the attractiveness increased as manure aged but started to decline after 3 weeks. Bioassays assessing the effect of manure age at the time of oviposition on larval development demonstrated that 1–3 week old manure supported larval development significantly better than fresh, 4, and 5 week old manure. In addition, adult fitness (body size) was significantly higher in flies from 1 and 2 week old manure comparing to that of all other treatments. Analysis of the bacterial community of aging horse manure by 454-pyrosequencing of 16S rDNA revealed a great reduction in bacterial diversity and richness from fresh to 1–5 week old manure and a major shift from strict anaerobes in fresh manure to facultative anaerobes and strict aerobes in aged manure. Overall, the microbial community of 2 and 3 week old horse manure with its dominant bacterial taxa Rhizobium, Devosia, and Brevundimonas stimulated stable fly oviposition the most and provided a suitable habitat for larval development. These bacteria represent the candidates for studies focused on better understanding of stable fly – microbial interactions.

Fibre digestibility, abundance of faecal bacteria and plasma acetate concentrations in overweight adult mares

The purpose of the present study was to compare digestibility of grass hay, faecal and plasma volatile fatty acid (VFA) concentrations, and faecal bacterial abundance in overweight and moderate-condition mares. Five overweight adult mixed-breed mares and five adult mixed-breed mares in moderate condition were housed individually and limit-fed orchard grass (Dactylis glomerata) hay at 20 g/kg body weight (as fed) daily for 14 d. Forage DM and fibre digestibility were determined using AOAC methods; digestible energy was measured using bomb calorimetry; plasma and faecal VFA concentrations were determined by use of GC and MS; faecal Firmicutes, Bacteroidetes, Fibrobacter succinogenes, Ruminococcus flavefaciens and total bacteria abundance was determined by quantitative real-time PCR using previously designed phylum-specific 16S ribosomal RNA gene primers. No differences in hay digestibility, faecal VFA concentrations or faecal bacterial abundance were detected between overweight and moderate-condition mares. Mean plasma acetate concentrations were higher (P = 0·03) in overweight (1·55 (range 1·43-1·65) mmol/l) v. moderate-condition (1·39 (range 1·22-1·47) mmol/l) mares. We conclude that the higher plasma acetate in overweight mares should be further investigated as a potential link between gut microbes and obesity in horses.

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

Propionate is produced in the human large intestine by microbial fermentation and may help maintain human health. We have examined the distribution of three different pathways used by bacteria for propionate formation using genomic and metagenomic analysis of the human gut microbiota and by designing degenerate primer sets for the detection of diagnostic genes for these pathways. Degenerate primers for the acrylate pathway (detecting the lcdA gene, encoding lactoyl-CoA dehydratase) together with metagenomic mining revealed that this pathway is restricted to only a few human colonic species within the Lachnospiraceae and Negativicutes. The operation of this pathway for lactate utilisation in Coprococcus catus (Lachnospiraceae) was confirmed using stable isotope labelling. The propanediol pathway that processes deoxy sugars such as fucose and rhamnose was more abundant within the Lachnospiraceae (based on the pduP gene, which encodes propionaldehyde dehydrogenase), occurring in relatives of Ruminococcus obeum and in Roseburia inulinivorans. The dominant source of propionate from hexose sugars, however, was concluded to be the succinate pathway, as indicated by the widespread distribution of the mmdA gene that encodes methylmalonyl-CoA decarboxylase in the Bacteroidetes and in many Negativicutes. In general, the capacity to produce propionate or butyrate from hexose sugars resided in different species, although two species of Lachnospiraceae (C. catus and R. inulinivorans) are now known to be able to switch from butyrate to propionate production on different substrates. A better understanding of the microbial ecology of short-chain fatty acid formation may allow modulation of propionate formation by the human gut microbiota.

Dietary supplementation with lactose or artificial sweetener enhances swine gut Lactobacillus population abundance

The commensal bacteria Lactobacillus are widely used as probiotic organisms conferring a heath benefit on the host. They have been implicated in promoting gut health via the stimulation of host immunity and anti-inflammatory responses, as well as protecting the intestinalmucosa against pathogen invasion. Lactobacilli grow by fermenting sugars and starches and produce lactic acid as their primary metabolic product. For efficient utilisation of varied carbohydrates, lactobacilli have evolved diverse sugar transport and metabolic systems, which are specifically induced by their own substrates. Many bacteria are also capable of sensing and responding to changes in their environment. These sensory responses are often independent of transport or metabolism and are mediated through membrane-spanning receptor proteins. We employed DNA-based pyrosequencing technology to investigate the changes in the intestinal microbiota of piglets weaned to a diet supplemented with either a natural sugar, lactose or an artificial sweetener (SUCRAM®, consisting of saccharin and neohesperidin dihydrochalcone (NHDC); Pancosma SA). The addition of either lactose or saccharin/NHDC to the piglets' feed dramatically increased the caecal population abundance of Lactobacillus, with concomitant increases in intraluminal lactic acid concentrations. This is the first report of the prebiotic-like effects of saccharin/NHDC, an artificial sweetener, being able to influence the commensal gut microbiota. The identification of the underlying mechanism(s) will assist in designing nutritional strategies for enhancing gut immunity and maintaining gut health.

Identification of a core bacterial community within the large intestine of the horse

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

Strong stability and host specific bacterial community in faeces of ponies

The horse, as a hindgut fermenter, is reliant on its intestinal bacterial population for efficient diet utilisation. However, sudden disturbance of this population can result in severe colic or laminitis, both of which may require euthanasia. This study therefore aimed to determine the temporal stability of the bacterial population of faecal samples from six ponies maintained on a formulated high fibre diet. Bacterial 16S rRNA terminal restriction fragment length polymorphism (TRFLP) analyses of 10 faecal samples collected from 6 ponies at regular intervals over 72 hour trial periods identified a significant pony-specific profile (P<0.001) with strong stability. Within each pony, a significantly different population was found after 11 weeks on the same diet (P<0.001) and with greater intra-individual similarity. Total short chain fatty acid (SCFA) concentration increased in all ponies, but other changes (such as bacterial population diversity measures, individual major SCFA concentration) were significant and dependent on the individual. This study is the first to report the extent of stability of microbes resident in the intestinal tract as represented with such depth and frequency of faecal sampling. In doing so, this provides a baseline from which future trials can be planned and the extent to which results may be interpreted.

The equine intestinal microbiome

The equine intestinal tract contains a complex microbial population (microbiota) that plays an important role in health and disease. Despite the undeniable importance of a 'normal' microbiota, understanding of the composition and function of this population is currently limited. As methods to characterize the microbiota and its genetic makeup (the microbiome) have evolved, the composition and complexity of this population are starting to be revealed. As is befitting a hindgut fermenter, members of the Firmicutes phylum appear to predominate, yet there are significant populations of numerous other phyla. The microbiome appears to be profoundly altered in certain disease states, and better understanding of these alterations may offer hope for novel preventive and therapeutic measures. The development and increasing availability of next generation sequencing and bioinformatics methods offer a revolution in microbiome evaluation and it is likely that significant advances will be made in the near future. Yet, proper use of these methods requires further study of basic aspects such as optimal testing protocols, the relationship of the fecal microbiome to more proximal locations where disease occurs, normal intra- and inter-horse variation, seasonal variation, and similar factors.

'Candidatus Arthromitus' revised: segmented filamentous bacteria in arthropod guts are members of Lachnospiraceae

The name Arthromitus has been applied collectively to conspicuous filamentous bacteria found in the hindguts of termites and other arthropods. First observed by Joseph Leidy in 1849, the identity of these filaments has remained contentious. While Margulis and colleagues declared them to be a life stage of Bacillus cereus, others have assumed them to belong to the same lineage as the segmented filamentous bacteria (SFB) from vertebrate guts, a group that has garnered much attention due to their unique ability to specifically modulate their host's immune response. Both SFB and Arthromitus filaments from arthropod guts were grouped under provisional name 'Candidatus Arthromitus' by Snel and colleagues as they share a striking similarity in terms of their morphology and close contact to the host gut wall. While SFB form a distinct lineage within the family Clostridiaceae, the identity of the filaments from arthropod guts remains elusive. Using whole-genome amplification of single filaments capillary picked from termite guts and fluorescence in situ hybridization of 16S rRNA with group-specific oligonucleotide probes, we show that they represent a monophyletic lineage within the family Lachnospiraceae distinct from that of SFB. Therefore, 'Candidatus Arthromitus' can no longer be used for both groups. Given the historic precedence, we propose to reserve this name for the filaments that were originally described by Leidy. For the SFB from vertebrate guts, we propose the provisional name 'Candidatus Savagella' in honour of the American gut microbiologist Dwayne C. Savage, who was the first to describe that important bacterial group.

The Fibrobacteres: an important phylum of cellulose-degrading bacteria

The phylum Fibrobacteres currently comprises one formal genus, Fibrobacter, and two cultured species, Fibrobacter succinogenes and Fibrobacter intestinalis, that are recognised as major bacterial degraders of lignocellulosic material in the herbivore gut. Historically, members of the genus Fibrobacter were thought to only occupy mammalian intestinal tracts. However, recent 16S rRNA gene-targeted molecular approaches have demonstrated that novel centres of variation within the genus Fibrobacter are present in landfill sites and freshwater lakes, and their relative abundance suggests a potential role for fibrobacters in cellulose degradation beyond the herbivore gut. Furthermore, a novel subphylum within the Fibrobacteres has been detected in the gut of wood-feeding termites, and proteomic analyses have confirmed their involvement in cellulose hydrolysis. The genome sequence of F. succinogenes rumen strain S85 has recently suggested that within this group of organisms a "third" way of attacking the most abundant form of organic carbon in the biosphere, cellulose, has evolved. This observation not only has evolutionary significance, but the superior efficiency of anaerobic cellulose hydrolysis by Fibrobacter spp., in comparison to other cellulolytic rumen bacteria that typically utilise membrane-bound enzyme complexes (cellulosomes), may be explained by this novel cellulase system. There are few bacterial phyla with potential functional importance for which there is such a paucity of phenotypic and functional data. In this review, we highlight current knowledge of the Fibrobacteres phylum, its taxonomy, phylogeny, ecology and potential as a source of novel glycosyl hydrolases of biotechnological importance.

Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons

The diversity of the equine fecal bacterial community was evaluated using pyrosequencing of 16S rRNA gene amplicons. Fecal samples were obtained from horses fed cool-season grass hay. Fecal bacteria were characterized by amplifying the V4 region of bacterial 16S rRNA gene. Of 5898 mean unique sequences, a mean of 1510 operational taxonomic units were identified in the four fecal samples. Equine fecal bacterial richness was higher than that reported in humans, but lower than that reported in either cattle feces or soil. Bacterial classified sequences were assigned to 16 phyla, of which 10 were present in all samples. The largest number of reads belonged to Firmicutes (43.7% of total bacterial sequences), Verrucomicrobia (4.1%), Proteobacteria (3.8%), and Bacteroidetes (3.7%). The less abundant Actinobacteria, Cyanobacteria, and TM7 phyla presented here have not been previously described in the gut contents or feces of horses. Unclassified sequences represented 38.1% of total bacterial sequences; therefore, the equine fecal microbiome diversity is likely greater than that described. This is the first study to characterize the fecal bacterial community in horses by the use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the fecal microbiota of forage-fed horses.

Alterations in microbiota and fermentation products in equine large intestine in response to dietary variation and intestinal disease

We aimed to determine the effects of variations in dietary composition on equine gut microbiota and their fermentation products, and proposed that dietary modifications profoundly affect microbial ecosystems and their metabolites. Bacterial communities within the large intestine of three groups of horses were compared using oligonucleotide-RNA hybridisation methodology. Each group consisting of six horses was maintained on (1) a grass-only diet, (2) a concentrate diet (i.e. supplemented with hydrolysable carbohydrates) and (3) a concentrate diet but horses were affected by simple colonic obstruction and distension (SCOD), a prevalent form of dietary-induced intestinal disease. We show that in response to dietary change and intestinal disease, there is a progressive and significant increase in Lachnospiraceae, the Bacteroidetes assemblage and the lactic acid-producing, Bacillus-Lactobacillus-Streptococcus (BLS) group. In contrast, there is a corresponding decrease in the proportion of obligate fibrolytic, acid-intolerant bacteria, Fibrobacter and Ruminococcaceae. Assessment of monocarboxylic acids indicated that there are significantly higher concentrations of lactic acid in the colonic contents of horses maintained on a concentrate diet and those suffering from SCOD, correlating with the observed increase in the population abundance of the BLS group. However, the population size of the Veillonellaceae (lactate utilisers) remained constant in each study group. The inability of this group to respond to increased lactic acid may be a contributory factor to the build-up of lactic acid observed in horses fed a concentrate diet and those suffering from SCOD.

Microbial events in the hindgut during carbohydrate-induced equine laminitis

Equine laminitis is the most serious foot disease of the horse, often resulting in death or euthanasia. Laminitis has long been recognized as an affliction of horses, as has the association of this condition with the ingestion of carbohydrates. Research into the pathophysiology of this condition has been facilitated by the development of reliable models for experimentally inducing laminitis, and DNA-based techniques for profiling complex microbiomes have dramatically increased the knowledge of the microbiology of this disease. Recent studies have provided substantial evidence showing equine hindgut streptococcal species to be the most likely causative agent. Although these studies are not definitive, they provide the foundations for future work to determine the source of laminitis trigger factors and their mechanisms of action.

Oral biofilm architecture on natural teeth

Periodontitis and caries are infectious diseases of the oral cavity in which oral biofilms play a causative role. Moreover, oral biofilms are widely studied as model systems for bacterial adhesion, biofilm development, and biofilm resistance to antibiotics, due to their widespread presence and accessibility. Despite descriptions of initial plaque formation on the tooth surface, studies on mature plaque and plaque structure below the gum are limited to landmark studies from the 1970s, without appreciating the breadth of microbial diversity in the plaque. We used fluorescent in situ hybridization to localize in vivo the most abundant species from different phyla and species associated with periodontitis on seven embedded teeth obtained from four different subjects. The data showed convincingly the dominance of Actinomyces sp., Tannerella forsythia, Fusobacterium nucleatum, Spirochaetes, and Synergistetes in subgingival plaque. The latter proved to be new with a possibly important role in host-pathogen interaction due to its localization in close proximity to immune cells. The present study identified for the first time in vivo that Lactobacillus sp. are the central cells of bacterial aggregates in subgingival plaque, and that Streptococcus sp. and the yeast Candida albicans form corncob structures in supragingival plaque. Finally, periodontal pathogens colonize already formed biofilms and form microcolonies therein. These in vivo observations on oral biofilms provide a clear vision on biofilm architecture and the spatial distribution of predominant species.

Composition of the landfill microbial community as determined by application of domain- and group-specific 16S and 18S rRNA-targeted oligonucleotide probes

The microbial community composition of colonized cotton and leachate samples from a landfill was quantified using small subunit (SSU) rRNA probes (quantitative rRNA hybridization). Relative quantification of bacteria, eukaryotes, and archaea revealed variations in the landfill microbial community between samples from different areas of the landfill site and indicated the presence of potentially novel archaea. Anaerobic fungi were quantified in rumen fluid samples but were not sufficiently abundant for direct detection in the landfill samples.

Detection of spatial fluctuations of non-point source fecal pollution in coral reef surrounding waters in southwestern Puerto Rico using PCR-based assays

Human fecal contamination of coral reefs is a major cause of concern. Conventional methods used to monitor microbial water quality cannot be used to discriminate between different fecal pollution sources. Fecal coliforms, enterococci, and human-specific Bacteroides (HF183, HF134), general Bacteroides-Prevotella (GB32), and Clostridium coccoides group (CP) 16S rDNA PCR assays were used to test for the presence of non-point source fecal contamination across the southwestern Puerto Rico shelf. Inshore waters were highly turbid, consistently receiving fecal pollution from variable sources, and showing the highest frequency of positive molecular marker signals. Signals were also detected at offshore waters in compliance with existing microbiological quality regulations. Phylogenetic analysis showed that most isolates were of human fecal origin. The geographic extent of non-point source fecal pollution was large and impacted extensive coral reef systems. This could have deleterious long-term impacts on public health, local fisheries and in tourism potential if not adequately addressed.

In vitro and in vivo effects of hydrolysates from conglycinin on intestinal microbial community of mice after Escherichia coli infection

AIMS

To detect the effect of pepsin-hydrolysate conglycinin (PTC) on the growth of Escherichia coli O(138)in vitro, and investigate the effect of PTC on intestinal microbial community of mice after E. coli infection.

METHODS AND RESULTS

Serial dilution method was used to detect the antibacterial activity of PTC in 96-well cell-cultivated plates. Fifty-five KM mice were randomly assigned to five groups: normal, feeding-E. coli control, HCl-full hydrolysis of conglycinin, conglycinin and PTC. Orally administrated with hydrolysates from conglycinin for 21 days, each mouse was fed with 2 x 10(8) CFU ml(-1) of E. coli O(138) on the 22nd day. The mice activities were monitored and polymerase chain reaction-denaturing gradient gel electrophoresis was used to analyse the microbial community in mice faeces. The results showed that PTC could inhibit growth of E. coli O(138) at nitrogen concentrations of more than 520 mg l(-1). There was high similarity of intestinal microbial community in mice between PTC and normal groups.

CONCLUSION

PTC inhibits growth of E. coli O(138), keeps mice healthy following oral administration of E. coli infection and maintains a balanced active microbial community in their gastrointestinal tract.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrated the antibacterial activity of PTC against E. coli and its ability to maintain healthy intestinal microbial community in mice even after they were infected with E. coli. This observation is significant in the application of PTC to prevent gastrointestinal diseases caused by E. coli and unbalanced intestinal microflora.

Molecular ecological analysis of the gastrointestinal microbiota: a review

The gastrointestinal (GI) microbiota of mammals is characterized by its high population density, wide diversity and complexity of interactions. While all major groups of microbes are represented, bacteria predominate. Importantly, bacterial cells outnumber animal (host) cells by a factor of ten and have a profound influence on nutritional, physiological and immunological processes in the host animal. Our knowledge of the molecular and cellular bases of host-microbe interactions is limited, though critically needed to determine if and how the GI microbiota contributes to various enteric disorders in humans and animals. Traditionally, GI bacteria have been studied via cultivation-based techniques, which are labor intensive and require previous knowledge of individual nutritional and growth requirements. Recently, findings from culture-based methods have been supplemented with molecular ecology techniques that are based on the 16S rRNA gene. These techniques enable characterization and quantification of the microbiota, while also providing a classification scheme to predict phylogenetic relationships. The choice of a particular molecular-based approach depends on the questions being addressed. Clone libraries can be sequenced to identify the composition of the microbiota, often to the species level. Microbial community structure can be analyzed via fingerprinting techniques, while dot blot hybridization or fluorescent in situ hybridization can measure abundance of particular taxa. Emerging approaches, such as those based on functional genes and their expression and the combined use of stable isotopes and biomarkers, are being developed and optimized to study metabolic activities of groups or individual organisms in situ. Here, a critical summary is provided of current molecular ecological approaches for studying the GI microbiota.

Phylogenetic analysis of fiber-associated rumen bacterial community and PCR detection of uncultured bacteria

The fiber-associated rumen bacterial community was phylogenetically examined by analysis of 16S rRNA gene (16S rDNA) sequences. Hay stems of orchardgrass and alfalfa were incubated for 6 and 20 h, respectively in the rumen of two different sheep, and total DNA was extracted from the incubated stems to clone bacterial 16S rDNAs using polymerase chain reaction (PCR). Of 91 such clones, 21 showed more than 97% sequence similarity with known isolates, 32 clones had 90-97% similarity with known sequences, and for the remaining 38 clones, the similarity was less than 90%. The majority of clones fell into the Cytophaga-Flavobacter-Bacteroides and low G+C Gram-positive bacterial phyla (43 and 44%, respectively). Prevotella-related and Butyrivibrio fibrisolvens-related sequences formed large clusters in the phylogenetic tree. Unknown sequences were found to form three unique clusters, one of which was suggested by semi-quantitative PCR to be more prevalent in the rumen receiving a high alfalfa diet.