Enumeration of anaerobic bacterial microflora of the equine gastrointestinal tract

Effects of concentrate levels on intestinal fermentation and the microbial profile in Japanese draft horses

In racehorses, feeding a high-concentrate diet could cause abnormal fermentation in the hindgut. This feeding management regime is not suitable for the nutritional physiology of horses. However, studies on the hindgut environment have yet to be reported in Japanese draft horses, so feeding management needs to be investigated in these horses. Therefore, the objective of this study was to investigate the effects of a high-concentrate diet on hindgut fermentation in Japanese draft horses. Feces were collected from 20 male Japanese draft horses managed by two stables with different feeding designs (65% weight ratio of concentrate feed, HC; 50% weight ratio of concentrate, MC), and fecal metabolic characteristics and the microbiome were analyzed. Higher lactate concentrations and lower fecal pH levels were observed in the HC group (P=0.0011, P=0.0192, respectively). Fecal microbiome analysis revealed a decrease in microbial diversity (P=0.0360) and an increase in the relative abundance of Streptococcus lutetiensis/equinus/infantarius (P=0.0011) in the HC group. On the other hand, fibrolytic bacteria in the MC group had similarities with Clostridium sacchalolyticum and Ruminococcus albus. This study revealed that overfeeding of concentrates induced abnormal fermentation in the hindgut of Japanese draft horses. This suggests that the establishment of a feeding design based on not only the chemical compositions of feeds but also microbial dynamics is needed.

Gastro-Intestinal Microbiota in Equines and Its Role in Health and Disease: The Black Box Opens

Horses are large non-ruminant herbivores and rely on microbial fermentation for energy, with more than half of their maintenance energy requirement coming from microbial fermentation occurring in their enlarged caecum and colon. To achieve that, the gastro-intestinal tract (GIT) of horses harbors a broad range of various microorganisms, differing in each GIT segment, which are essential for efficient utilization of feed, especially to use nutrients that are not or little degraded by endogenous enzymes. In addition, like in other animal species, the GIT microbiota is in permanent interplay with the host's cells and is involved in a lot of functions among which inflammation, immune homeostasis, and energy metabolism. As for other animals and humans, the horse gut microbiome is sensitive to diet, especially consumption of starch, fiber, and fat. Age, breeds, stress during competitions, transportation, and exercise may also impact the microbiome. Because of its size and its complexity, the equine GIT microbiota is prone to perturbations caused by external or internal stressors that may result in digestive diseases like gastric ulcer, diarrhea, colic, or colitis, and that are thought to be linked with systemic diseases like laminitis, equine metabolic syndrome or obesity. Thus, in this review we aim at understanding the common core microbiome -in terms of structure and function- in each segment of the GIT, as well as identifying potential microbial biomarkers of health or disease which are crucial to anticipate putative perturbations, optimize global practices and develop adapted nutritional strategies and personalized nutrition.

The Role of Yeast Saccharomyces cerevisiae in Supporting Gut Health in Horses: An Updated Review on Its Effects on Digestibility and Intestinal and Fecal Microbiota

To support the overall health of horses, it is essential to maintain an optimal gut health (GH) status, which encompasses several physiological and functional aspects, including the balance and functionality of intestinal microbial populations and, accordingly, the effective digestion and absorption of nutrients. Numerous biotic and abiotic stressors can lead to an imbalance of GH, such as the quality of forages and the composition of diet, e.g., the inclusion of high energy-dense feeds to meet the energy requirements of performance horses. To support the digestive function and the intestinal microbial populations, the diet can be supplemented with feed additives, such as probiotic yeasts, that promote the ability of cellulolytic bacteria in the hindgut to digest the available fiber fractions, finally increasing feed efficiency. Among the different yeasts available, S. cerevisiae is the most used in horses' nutrition; however, results of digestibility trials, as well as data on intestinal and fecal microbial populations, are sometimes contradictory. Therefore, the purpose of this review is to summarize the effects of S. cerevisiae on in vivo and in vitro digestibility, providing an updated overview of its effects on the intestinal and fecal microbial population.

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.

Gut Microbiota Manipulation in Foals-Naturopathic Diarrhea Management, or Unsubstantiated Folly?

Diarrhea in foals is a problem of significant clinical and economic consequence, and there are good reasons to believe microbiota manipulation can play an important role in its management. However, given the dynamic development of the foal microbiota and its importance in health and disease, any prophylactic or therapeutic efforts to alter its composition should be evidence based. The few clinical trials of probiotic preparations conducted in foals to date show underwhelming evidence of efficacy and a demonstrated potential to aggravate rather than mitigate diarrhea. Furthermore, recent studies have affirmed that variable but universally inadequate quality control of probiotics enables inadvertent administration of toxin-producing or otherwise pathogenic bacterial strains, as well as strains bearing transferrable antimicrobial resistance genes. Consequently, it seems advisable to approach probiotic therapy in particular with caution for the time being. While prebiotics show initial promise, an even greater scarcity of clinical trials makes it impossible to weigh the pros and cons of their use. Advancing technology will surely continue to enable more detailed and accurate mapping of the equine adult and juvenile microbiota and potentially elucidate the complexities of causation in dysbiosis and disease. In the meantime, fecal microbiota transplantation may be an attractive therapeutic shortcut, allowing practitioners to reconstruct a healthy microbiota even without fully understanding its constitution.

Effects of Aleurone Supplementation on Glucose-Insulin Metabolism and Gut Microbiome in Untrained Healthy Horses

Aleurone, a layer of the bran fraction, is deemed to be responsible for the positive health effects associated with the consumption of whole-grain products. Studies on rodents, pigs, and humans report beneficial effects of aleurone in five main areas: the reduction of oxidative stress, immunomodulatory effects, modulation of energy management, digestive health, and the storage of vitamins and minerals. Our study is the first aleurone supplementation study performed in horses. The aim of this study was to investigate the effect of an increase in the dose levels of aleurone on the postprandial glucose-insulin metabolism and the gut microbiome in untrained healthy horses. Seven adult Standardbred horses were supplemented with four different dose levels of aleurone (50, 100, 200, and 400 g/day for 1 week) by using a Latin square model with a 1-week wash out in between doses. On day 7 of each supplementation week, postprandial blood glucose-insulin was measured and fecal samples were collected. 16S ribosomal RNA (rRNA) gene sequencing was performed and QIIME2 software was used for microbiome analysis. Microbial community function was assessed by using the predictive metagenome analysis tool Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and using the Metacyc database of metabolic pathways. The relative abundancies of a pathway were analyzed by using analysis of composition of microbiomes (ANCOM) in R. There was a significant dose-dependent increase in the postprandial time to peak of glucose (p = 0.030), a significant delay in the time to peak of insulin (p = 0.025), and a significant decrease in both the insulin peak level (p = 0.049) and insulin area under the curve (AUC) (p = 0.019) with increasing dose levels of aleurone, with a consideration of 200 g being the lowest significant dose. Alpha diversity and beta diversity of the fecal microbiome showed no significant changes. Aleurone significantly decreased the relative abundance of the genera Roseburia, Shuttleworthia, Anaerostipes, Faecalibacter, and Succinovibrionaceae. The most pronounced changes in the relative abundance at phyla level were seen in Firmicutes and Verrucomicrobia (downregulation) and Bacteroidetes and Spirochaetes (upregulation). The PICRUSt analysis shows that aleurone induces a downregulation of the degradation of L-glutamate and taurine and an upregulation of the three consecutive pathways of the phospholipid membrane synthesis of the Archaea domain. The results of this study suggest a multimodal effect of aleurone on glucose-insulin metabolism, which is most likely to be caused by its effect on feed texture and subsequent digestive processing; and a synergistic effect of individual aleurone components on the glucose-insulin metabolism and microbiome composition and function.

Priming for welfare: gut microbiota is associated with equitation conditions and behavior in horse athletes

We simultaneously measured the fecal microbiota and multiple environmental and host-related variables in a cohort of 185 healthy horses reared in similar conditions during a period of eight months. The pattern of rare bacteria varied from host to host and was largely different between two time points. Among a suite of variables examined, equitation factors were highly associated with the gut microbiota variability, evoking a relationship between gut microbiota and high levels of physical and mental stressors. Behavioral indicators that pointed toward a compromised welfare state (e.g. stereotypies, hypervigilance and aggressiveness) were also associated with the gut microbiota, reinforcing the notion for the existence of the microbiota-gut-brain axis. These observations were consistent with the microbiability of behaviour traits (> 15%), illustrating the importance of gut microbial composition to animal behaviour. As more elite athletes suffer from stress, targeting the microbiota offers a new opportunity to investigate the bidirectional interactions within the brain gut microbiota axis.

Characterization of the normal equine conjunctival bacterial community using culture-independent methods

BACKGROUND

The equine conjunctival microbiota has often been reported to be dominated by Gram-positive species such as Staphylococcus sp., Bacillus sp., and Corynebacterium sp. However, traditional culture-based methods can only recover a fraction of the bacterial species present in the sample.

OBJECTIVES

This pilot study aimed at exploring the diversity of the equine conjunctival microbiota using culture-independent methods.

STUDY DESIGN

Eight horses were included in this study, and only eyes with normal ophthalmic examination (n = 15 eyes) were sampled.

METHODS

Conjunctival biopsies (culture-independent) were collected, and DNA was extracted from the tissues. Bacterial communities in conjunctival biopsies were characterized by next-generation sequencing of the 16S rRNA genes. Individual reads were ascribed to operational taxonomic units (OTUs) using BLASTn and Greengenes databases. Species richness, evenness, and Good's coverage were determined for each conjunctiva-associated microbial community.

RESULTS

Culture-independent samples produced a total of 329 bacterial OTUs. The main OTUs identified in the study belonged to the Gram-negative species Ralstonia mannitolilytica (88.0%), Nicoletella semolina (3.3%), and Pseudomonas tolaasii (1.5%).

CONCLUSIONS

Contrary to previously published data based on culture-dependent methods, the horse eye microbial community was dominated by Gram-negative bacteria of the phylum Proteobacteria.

Inter-breed diversity and temporal dynamics of the faecal microbiota in healthy horses

Understanding gut microbiota similarities and differences across breeds in horses has the potential to advance approaches aimed at personalized microbial modifications, particularly those involved in improving sport athletic performance. Here, we explore whether faecal microbiota composition based on faecal 16S ribosomal RNA gene sequencing varies across six different sport breeds at two time points 8 months apart within a cohort of 189 healthy horses cared for under similar conditions. Lusitano horses presented the smallest and Hanoverians the greatest bacterial diversity. We found subtle but significant differences in β-diversity between Lusitano, Anglo Arabian and the central European breeds, and we reproduced these results across the two time points. Repeat sampling of subjects showed community to be temporally more stable in Lusitano and Anglo Arabian breeds. Additionally, we found that 27 genera significantly varied in abundance across breeds. Overall, 33% of these taxa overlapped with previously identified taxa that were associated with genetic variation in humans or other species. However, a non-significant correlation was observed between microbial composition and the host pedigree-based kinship. Despite a notable variation in the diversity and composition of the faecal microbiota, breed exerted limited effects on the equine faecal microbiota.

Modification of the equine gastrointestinal microbiota by Jerusalem artichoke meal supplementation

The objective of this study was to investigate the impact of natural prebiotic active compounds on the microbial composition in different regions of the equine gastrointestinal tract. Twelve adult horses (body weight [bwt] 534 ± 64.5 kg; age 14 ± 7.5 years) were randomly divided into two feeding groups. Six horses received a basal diet consisting of 1.5 kg hay/100 kg bwt x d^-1 and oat grains equal to 1.19 g starch/kg bwt x d^-1, supplemented with Jerusalem artichoke meal providing prebiotic fructooligosaccharides + inulin in a quantity of 0.15 g/kg bwt x d^-1. The remaining horses received a placebo added to the basal diet. The horses were fed for 21 d and euthanized at the end of the feeding period. Digesta samples from different parts of the gastrointestinal tract were taken, DNA extracted and the V1-V2 region of the 16S rRNA gene amplified. Supplementation with the prebiotic increased the relative abundance of Lactobacillus (P < 0.05), with a concurrent reduction of the relative abundance of Streptococcus mainly in the stomach (P < 0.05). In the hindgut, the supplemental prebiotic also increased the relative abundance of Lactobacillus but further reduced the relative abundance of fibrolytic bacteria, specifically the unclassified members of the families Lachnospiraceae (P < 0.05) and Ruminococcaceae. The relative abundance of the genus Ruminococcus increased solely in the caecum and colon transversum. Overall, the addition of the prebiotic significantly increased the diversity in nearly all parts of the gastrointestinal tract (P < 0.05). The feeding of this natural prebiotic compound to horses had an impact on the microbial community in the entire gastrointestinal tract. Furthermore, the effect on the bacterial community in the foregut (especially the stomach) was more pronounced in comparison to the effect in the hindgut. Therefore, the impact on stomach health should be carefully considered.

Unraveling the effects of the gut microbiota composition and function on horse endurance physiology

An integrated analysis of gut microbiota, blood biochemical and metabolome in 52 endurance horses was performed. Clustering by gut microbiota revealed the existence of two communities mainly driven by diet as host properties showed little effect. Community 1 presented lower richness and diversity, but higher dominance and rarity of species, including some pathobionts. Moreover, its microbiota composition was tightly linked to host blood metabolites related to lipid metabolism and glycolysis at basal time. Despite the lower fiber intake, community type 1 appeared more specialized to produce acetate as a mean of maintaining the energy supply as glucose concentrations fell during the race. On the other hand, community type 2 showed an enrichment of fibrolytic and cellulolytic bacteria as well as anaerobic fungi, coupled to a higher production of propionate and butyrate. The higher butyrate proportion in community 2 was not associated with protective effects on telomere lengths but could have ameliorated mucosal inflammation and oxidative status. The gut microbiota was neither associated with the blood biochemical markers nor metabolome during the endurance race, and did not provide a biomarker for race ranking or risk of failure to finish the race.

Equine Contribution in Methane Emission and Its Mitigation Strategies

Greenhouses gas emission mitigation is a very important aspect of earth sustainability with greenhouse gasses reduction, a focus of agricultural and petrochemical industries. Methane is produced in nonruminant herbivores such as horses because they undergo hindgut fermentation. Although equine produce less methane than ruminant, increasing population of horses might increase their contribution to the present 1.2 to 1.7 Tg, estimate. Diet, feeding frequency, season, genome, and protozoa population influence methane production equine. In population, Methanomicrobiales, Methanosarcinales, Methanobacteriales, and Methanoplasmatales are the clade identified in equine. Methanocorpusculum labreanum is common among hindgut fermenters like horses and termite. Naturally, acetogenesis and interrelationship between the host and the immune-anatomical interaction are responsible for the reduced methane output in horses. However, to reduce methane output in equine, and increase energy derived from feed intake, the use of biochar, increase in acetogens, inclusion of fibre enzymes and plant extract, and recycling of fecal energy through anaerobic gas fermentation. These might be feasible ways to reducing methane contribution from horse and could be applied to ruminants too.

Strongyle Infection and Gut Microbiota: Profiling of Resistant and Susceptible Horses Over a Grazing Season

Gastrointestinal strongyles are a major threat to horses' health and welfare. Given that strongyles inhabit the same niche as the gut microbiota, they may interact with each other. These beneficial or detrimental interactions are unknown in horses and could partly explain contrasted susceptibility to infection between individuals. To address these questions, an experimental pasture trial with 20 worm-free female Welsh ponies (10 susceptible (S) and 10 resistant (R) to parasite infection) was implemented for 5 months. Fecal egg counts (FEC), hematological and biochemical data, body weight and gut microbiological composition were studied in each individual after 0, 24, 43, 92 and 132 grazing days. R and S ponies displayed divergent immunological profiles and slight differences in microbiological composition under worm-free conditions. After exposure to natural infection, the predicted R ponies exhibited lower FEC after 92 and 132 grazing days, and maintained higher levels of circulating monocytes and eosinophils, while lymphocytosis persisted in S ponies. Although the overall gut microbiota diversity and structure remained similar during the parasite infection between the two groups, S ponies exhibited a reduction of bacteria such as Ruminococcus, Clostridium XIVa and members of the Lachnospiraceae family, which may have promoted a disruption of mucosal homeostasis at day 92. In line with this hypothesis, an increase in pathobionts such as Pseudomonas and Campylobacter together with changes in several predicted immunological pathways, including pathogen sensing, lipid metabolism, and activation of signal transduction that are critical for the regulation of immune system and energy homeostasis were observed in S relative to R ponies. Moreover, S ponies displayed an increase in protozoan concentrations at day 92, suggesting that strongyles and protozoa may contribute to each other's success in the equine intestines. It could also be that S individuals favor the increase of these carbohydrate-degrading microorganisms to enhance the supply of nutrients needed to fight strongyle infection. Overall, this study provides a foundation to better understand the mechanisms that underpin the relationship between equines and natural strongyle infection. The profiling of horse immune response and gut microbiota should contribute to the development of novel biomarkers for strongyle infection.

Identification of hypoglycin A binding adsorbents as potential preventive measures in co-grazers of atypical myopathy affected horses

BACKGROUND

Intestinal absorption of hypoglycin A (HGA) and its metabolism are considered major prerequisites for atypical myopathy (AM). The increasing incidence and the high mortality rate of AM urgently necessitate new therapeutic and/or preventative approaches.

OBJECTIVES

To identify a substance for oral administration capable of binding HGA in the intestinal lumen and effectively reducing the intestinal absorption of the toxin.

STUDY DESIGN

Experimental in vitro study.

METHODS

Substances commonly used in equine practice (activated charcoal composition, di-tri-octahedral smectite, mineral oil and activated charcoal) were tested for their binding capacity for HGA using an in vitro incubation method. The substance most effective in binding HGA was subsequently tested for its potential to reduce intestinal HGA absorption. Jejunal tissues of 6 horses were incubated in Ussing chambers to determine mucosal uptake, tissue accumulation, and serosal release of HGA in the presence and absence of the target substance. Potential intestinal metabolism in methylenecyclopropyl acetic acid (MCPA)-conjugates was investigated by analysing their concentrations in samples from the Ussing chambers.

RESULTS

Activated charcoal composition and activated charcoal were identified as potent HGA binding substances with dose and pH dependent binding capacity. There was no evidence of intestinal HGA metabolism.

MAIN LIMITATIONS

Binding capacity of adsorbents was tested in vitro using aqueous solutions, and in vivo factors such as transit time and composition of intestinal content, may affect adsorption capacity after oral administration.

CONCLUSIONS

For the first time, this study identifies substances capable of reducing HGA intestinal absorption. This might have major implications as a preventive measure in cograzers of AM affected horses but also in horses at an early stage of intoxication.

The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology

Weaning has been described as one of the most stressful events in the life of horses. Given the importance of the interaction between the gut-brain axis and gut microbiota under stress, we evaluated (i) the effect of two different weaning methods on the composition of gut microbiota across time and (ii) how the shifts of gut microbiota composition after weaning affect the host. A total of 34 foals were randomly subjected to a progressive (P) or an abrupt (A) weaning method. In the P method, mares were separated from foals at progressively increasing intervals every day, starting from five min during the fourth week prior to weaning and ending with 6 h during the last week before weaning. In the A method, mares and foals were never separated prior to weaning (0 d). Different host phenotypes and gut microbiota composition were studied across 6 age strata (days -30, 0, 3, 5, 7, and 30 after weaning) by 16S rRNA gene sequencing. Results revealed that the beneficial species belonging to Prevotella, Paraprevotella, and Ruminococcus were more abundant in the A group prior to weaning compared to the P group, suggesting that the gut microbiota in the A cohort was better adapted to weaning. Streptococcus, on the other hand, showed the opposite pattern after weaning. Fungal loads, which are thought to increase the capacity for fermenting the complex polysaccharides from diet, were higher in P relative to A. Beyond the effects of weaning methods, maternal separation at weaning markedly shifted the composition of the gut microbiota in all foals, which fell into three distinct community types at 3 days post-weaning. Most genera in community type 2 (i.e., Eubacterium, Coprococcus, Clostridium XI, and Blautia spp.) were negatively correlated with salivary cortisol levels, but positively correlated with telomere length and N-butyrate production. Average daily gain was also greater in the foals harboring a community type 2 microbiota. Therefore, community type 2 is likely to confer better stress response adaptation following weaning. This study identified potential microbial biomarkers that could predict the likelihood for physiological adaptations to weaning in horses, although causality remains to be addressed.

Functional Resilience and Response to a Dietary Additive (Kefir) in Models of Foregut and Hindgut Microbial Fermentation In Vitro

Stability in gut ecosystems is an important area of study that impacts on the use of additives and is related with several pathologies. Kefir is a fermented milk drink made with a consortium of yeast and bacteria as a fermentation starter, of which the use as additive in companion and livestock animals has increased in the last few years. To investigate the effect of kefir milk on foregut and hindgut digestive systems, an in vitro approach was followed. Either rumen fluid or horse fecal contents were used as a microbial inoculate and the inclusion of kefir (fresh, autoclaved, or pasteurized) was tested. Gas production over 72 h of incubation was recorded and pH, volatile fatty acids (VFAs), lactate and ammonia concentration as well as lactic acid (LAB) and acetic acid bacteria, and yeast total numbers were also measured. Both direct and indirect (by subtracting their respective blanks) effects were analyzed and a multivariate analysis was performed to compare foregut and hindgut fermentation models. Addition of kefir boosted the fermentation by increasing molar concentration of VFAs and ammonia and shifting the Acetate to Propionate ratio in both models but heat processing techniques like pasteurization or autoclaving influenced the way the kefir is fermented and reacts with the present microbiota. In terms of comparison between both models, the foregut model seems to be less affected by the inclusion of Kefir than the hindgut model. In terms of variability in the response, the hindgut model appeared to be more variable than the foregut model in the way that it reacted indirectly to the addition of different types of kefir.

Effects of liposomal-curcumin on five opportunistic bacterial strains found in the equine hindgut - preliminary study

Background

The horse intestinal tract is sensitive and contains a highly complex microbial population. A shift in the microbial population can lead to various issues such as inflammation and colic. The use of nutraceuticals in the equine industry is on the rise and curcumin is thought to possess antimicrobial properties that may help to minimize the proliferation of opportunistic bacteria.

Methods

Four cecally-cannulated horses were utilized to determine the optimal dose of liposomal-curcumin (LIPC) on reducing Streptococcus bovis/equinus complex (SBEC), Escherichia coli K-12, Escherichia coli general, Clostridium difficile, and Clostridium perfringens in the equine hindgut without adversely affecting cecal characteristics. In the first study cecal fluid was collected from each horse and composited for an in vitro, 24 h batch culture to examine LIPC at four different dosages (15, 20, 25, and 30 g) in a completely randomized design. A subsequent in vivo 4 × 4 Latin square design study was conducted to evaluate no LIPC (control, CON) or LIPC dosed at 15, 25, and 35 g per day (dosages determined from in vitro results) for 9 days on the efficacy of LIPC on selected bacterial strains, pH, and volatile fatty acids. Each period was 14 days with 9 d for acclimation and 5 d withdrawal period.

Results

In the in vitro study dosage had no effect (P ≥ 0.42) on Clostridium strains, but as the dose increased SBEC concentrations increased (P = 0.001). Concentrations of the E. coli strain varied with dose. In vivo, LIPC’s antimicrobial properties, at 15 g, significantly decreased (P = 0.02) SBEC when compared to 25 and 35 g dosages. C. perfringens decreased linearly (P = 0.03) as LIPC dose increased. Butyrate decreased linearly (P = 0.01) as LIPC dose increased.

Conclusion

Further studies should be conducted with a longer dosing period to examine the antimicrobial properties of curcumin without adversely affecting cecal characteristics.

Enteric Pathogens and Coinfections in Foals with and without Diarrhea

Diarrhea is a major clinical problem affecting foals up to 3 months of age. The aim of this study was to identify enteric microorganisms involved in monoinfections and coinfections and the associated virulence factors in healthy and diarrheic foals. Diarrheic (D) (n = 56) and nondiarrheic (ND) foals (n = 60) up to three months of age were studied. Fecal samples were analyzed for identification of infectious agents (microbiological culturing, molecular techniques, and microscopic analyses). Escherichia coli fimH (30% versus 25%), Salmonella spp. (25% versus 7%), Strongyloides westeri (25% versus 25%), Clostridium perfringens type A (21% versus 10%), E. coli ag43 (20% versus 35%), Strongylus (11% versus 18%), and vapA-positive Rhodococcus equi (5% versus 2%) were the most frequent enteric pathogens detected in D and ND foals, respectively. The frequency of toxin A-positive C. perfringens was significantly increased in the D (p = 0.033) compared with the ND animals. R. equi strains harboring virulent plasmids were also identified (VapA 85-kb type I and VapA 87-kb type I) in D and ND foals. Coinfections were observed in 46% of the D and 33% of the ND foals. Our results demonstrate the great diversity of enteric pathogens, virulence factors, and coinfections involved in enteric infections of foals.

A Microbiological Map of the Healthy Equine Gastrointestinal Tract

Horses are exquisitely sensitive to non-specific gastrointestinal disturbances as well as systemic and extraintestinal conditions related to gut health, yet minimal data are available regarding the composition of the microbiota present in the equine stomach, small intestine, and cecum and their relation to fecal microbiota. Moreover, there is minimal information regarding the concordance of the luminal and mucosal microbial communities throughout the equine gut. Illumina-based 16S rRNA gene amplicon sequencing of the luminal and mucosal microbiota present in seven regions of the gastrointestinal tract of nine healthy adult horses revealed a distinct compositional divide between the small and large intestines. This disparity in composition was more pronounced within the luminal contents, but was also detected within mucosal populations. Moreover, the uniformity of the gut microbiota was much higher in the cecum and colon relative to that in the stomach, jejunum and ileum, despite a significantly higher number of unique sequences detected in the colon. Collectively, the current data suggest that while colonic samples (a proxy for feces) may provide a reasonable profile of the luminal contents of the healthy equine large intestine, they are not informative with regard to the contents of the stomach or small intestine. In contrast to the distinct difference between the highly variable upper gastrointestinal tract microbiota and relatively uniform large bowel microbiota present within the lumen, these data also demonstrate a regional continuity present in mucosal microbial communities throughout the length of the equine gut.

Exercise training-induced changes in the gut microbiota of Standardbred racehorses

Exercise has a significant effect on different physiological systems in the body of human and animals. Only limited numbers of published studies in laboratory animals or humans have shown the effect of exercise on the gut microbiota, and no studies have shown this effect in horses. In this study, 8 horses (4 mares, 4 geldings) were exercise trained for 12 weeks, and 4 additional mares were used as a parallel seasonal control. To identify bacterial community changes over time for both groups, rectal faecal samples were collected, DNA was extracted, and the 16S rRNA gene (V3-V4) was sequenced using the Illumina Miseq platform. One-way ANOVA, Shannon diversity index, and Principal Coordinate Analysis (PCoA) were used to identify differences between and among samples. The exercise training group showed significant changes in the levels of Bacteroidetes, Proteobacteria, and Spirochaetes phyla (P<0.05), while there were no changes in the gut microbiota of the seasonal control group through the three months of the study (P>0.05). Moreover, with training two genera significantly changed in their relative abundance over time, namely Clostridium and Dysgonomonas (P<0.05). Dysgonomonas spp. was significantly changed in abundance during the exercise training period (P<0.05). Also Treponema spp. showed significant changes during the exercise training period (P<0.05). Shannon diversity index was decreased (P<0.05) in the exercise group at the beginning of the study, but then returned to pre-training levels. PCoA showed significant separation between time points of the exercise training group as far as the levels of genera and species (P<0.05) represented. Our results show that exercise training influences the gut microbiota, especially at the beginning of training.

Characterization of the microbial and biochemical profile of the different segments of the digestive tract in horses given two distinct diets

A first group of three horses was given diet 1 (D1) allowing 1180 g per 100 kg body weight (BW) of a pelleted food rich in fibre (P1) and 556 g per 100 kg BW of straw during a 20-day period to allow for adaptation. A second group of four horses were given diet 2 (D2) allowing 1180 g per 100 kg BW of a pelleted food rich in cereals (P2) and 1000 g per 100 kg BW of meadow hay during the same period. Digesta was collected from the stomach, duodenum, jejunum, ileum, caecum, right ventral colon, left ventral colon, left dorsal colon, right dorsal colon, and small colon, and faeces were collected under general anaesthesia 2·5 h after the ingestion of the morning pelleted meal. The concentration of total anaerobic, cellulolytic and lactic acid-utilizing bacteria, lactobacilli and streptococci were determined in all these segments except for the duodenum, left ventral colon, right dorsal colon and small colon. D-/L-lactic acid, volatile fatty acids and pH were measured in all anatomic segments of the digestive tract (from stomach to small colon). The caecal concentration of total anaerobic bacteria was the lowest (7·9 5 107colony-forming units (c f. u.) per ml), whereas that of the stomach was the highest (1·4 5 109c f. u. per ml) (P< 0·001). Cellulolytic bacteria did not exceed 3·0 5 102c f u. per ml in the ante-caecal segments whereas in the hindgut the average concentration was 5·3 x 105c f u. per ml (P< 0·001). Likewise, VFA concentrations were also greater in the large intestine (on average, 96·3 mmol/l v. 8·8 mmol/l in the ante-caecal segments) (P< 0·001), confirming the limited extent of fibre degradation in these ante-caecal segments. Lactobacilli, streptococci and lactate-utilizing bacteria colonized all the digestive tract; the stomach and the small intestine tended to host the greatest numbers of these bacteria, which suggests a high interference of micro-organisms with the digestion of readily fermentable carbohydrates. Compared with the other ante-caecal segments, the stomach ecosystem seemed the most affected by the composition of the last pelleted meal ingested: the concentrations of lactobacilli and lactate-utilizing bacteria were higher (P< 0·05) with P2. The lower concentration of D-/L-lactate with P2 (P< 0·05) was concomitant with a greater proportion of propionate (P< 0·05), probably related to a greater fermentation of lactate. In the large intestine of horses given D2, cellulolytic bacteria tended to be lower, whereas VFA concentrations were higher (P < 0·05). The lower [NDF/starch] ratio of D2 was probably less propitious for the proliferation of cellulolytic bacteria but was compensated by the higher cellulose intake brought by the hay.

Rapid Change of Microbiota Diversity in the Gut but Not the Hepatopancreas During Gonadal Development of the New Shrimp Model Neocaridina denticulata

During evolution of animals, their co-evolution with bacteria has generally been ignored. Recent studies have provided evidences that the symbiotic bacteria in the animal gut can either be essential or contributing to the plasticity of the host. The Crustacea includes crab, crayfish, lobster, and shrimp and represents the second largest subphylum on the planet. Although there are already studies investigating the intestinal bacterial communities in crustaceans, none of them has examined the microbiota in different parts of the digestive system during the gonad development of the host. Here, we utilized a new shrimp model Neocaridina denticulata and sequenced the 16S rRNA using the Ion Torrent platform to survey the bacterial populations colonizing the hepatopancreas, foregut, and intestine, including midgut and hindgut, of the early, mid, and late ovarian maturation stages of the shrimp. The predominant bacteria phylum was found to be Proteobacteria, with more than 80 % reads from the gut flora at the early gonad development belonged to a Coxiella-type bacterium. Distinct bacterial communities can be detected between the hepatopancreas and gut, although no significant difference could be revealed between the different regions of the gut investigated. Surprisingly, during the gonad development, bacterial diversity changed rapidly in the gut but not the hepatopancreas. This study provides the first evidence that microbiota modified differentially in specific regions of the digestive tract during gonadal development of crustaceans.

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.

An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction

Laminitis is a chronic, crippling disease triggered by the sudden influx of dietary starch. Starch reaches the hindgut resulting in enrichment of lactic acid bacteria, lactate accumulation, and acidification of the gut contents. Bacterial products enter the bloodstream and precipitate systemic inflammation. Hindgut lactate levels are normally low because specific bacterial groups convert lactate to short chain fatty acids. Why this mechanism fails when lactate levels rapidly rise, and why some hindgut communities can recover is unknown. Fecal samples from three adult horses eating identical diets provided bacterial communities for this in vitro study. Triplicate microcosms of fecal slurries were enriched with lactate and/or starch. Metabolic products (short chain fatty acids, headspace gases, and hydrogen sulfide) were measured and microbial community compositions determined using Illumina 16S rRNA sequencing over 12-hour intervals. We report that patterns of change in short chain fatty acid levels and pH in our in vitro system are similar to those seen in in vivo laminitis induction models. Community differences between microcosms with disparate abilities to clear excess lactate suggest profiles conferring resistance of starch-induction conditions. Where lactate levels recover following starch induction conditions, propionate and acetate levels rise correspondingly and taxa related to Megasphaeraelsdenii reach levels exceeding 70% relative abundance. In lactate and control cultures, taxa related to Veillonellamontpellierensis are enriched as lactate levels fall. Understanding these community differences and factors promoting the growth of specific lactate utilizing taxa may be useful to prevent acidosis under starch-induction conditions.

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.

Comparison of microbial populations in the small intestine, large intestine and feces of healthy horses using terminal restriction fragment length polymorphism

Background

The composition of the microbiota of the equine intestinal tract is complex. Determining whether the microbial composition of fecal samples is representative of proximal compartments of the digestive tract could greatly simplify future studies. The objectives of this study were to compare the microbial populations of the duodenum, ileum, cecum, colon and rectum (feces) within and between healthy horses, and to determine whether rectal (fecal) samples are representative of proximal segments of the gastrointestinal tract. Intestinal samples were collected from ten euthanized horses. 16S rRNA gene PCR-based TRFLP was used to investigate microbiota richness in various segments of the gastrointestinal tract, and dice similarity indices were calculated to compare the samples.

Results

Within horses large variations of microbial populations along the gastrointestinal tract were seen. The microbiota in rectal samples was only partially representative of other intestinal compartments. The highest similarity was obtained when feces were compared to the cecum. Large compartmental variations were also seen when microbial populations were compared between six horses with similar dietary and housing management.

Conclusion

Rectal samples were not entirely representative of intestinal compartments in the small or large intestine. This should be taken into account when designing studies using fecal sampling to assess other intestinal compartments. Similarity between horses with similar dietary and husbandry management was also limited, suggesting that parts of the intestinal microbiota were unique to each animal in this study.

Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis

Background

The nutrition and health of horses is closely tied to their gastrointestinal microflora. Gut bacteria break down plant structural carbohydrates and produce volatile fatty acids, which are a major source of energy for horses. Bacterial communities are also essential for maintaining gut homeostasis and have been hypothesized to contribute to various diseases including laminitis. We performed pyrosequencing of 16S rRNA bacterial genes isolated from fecal material to characterize hindgut bacterial communities in healthy horses and those with chronic laminitis.

Results

Fecal samples were collected from 10 normal horses and 8 horses with chronic laminitis. Genomic DNA was extracted and the V4-V5 segment of the 16S rRNA gene was PCR amplified and sequenced on the 454 platform generating a mean of 2,425 reads per sample after quality trimming. The bacterial communities were dominated by Firmicutes (69.21% control, 56.72% laminitis) and Verrucomicrobia (18.13% control, 27.63% laminitis), followed by Bacteroidetes, Proteobacteria, and Spirochaetes. We observed more OTUs per individual in the laminitis group than the control group (419.6 and 355.2, respectively, P = 0.019) along with a difference in the abundance of two unassigned Clostridiales genera (P = 0.03 and P = 0.01). The most abundant bacteria were Streptococcus spp., Clostridium spp., and Treponema spp.; along with unassigned genera from Subdivision 5 of Verrucomicrobia, Ruminococcaceae, and Clostridiaceae, which together constituted ~ 80% of all OTUs. There was a high level of individual variation across all taxonomic ranks.

Conclusions

Our exploration of the equine fecal microflora revealed higher bacterial diversity in horses with chronic laminitis and identification of two Clostridiales genera that differed in abundance from control horses. There was large individual variation in bacterial communities that was not explained in our study. The core hindgut microflora was dominated by Streptococcus spp., several cellulytic genera, and a large proportion of uncharacterized OTUs that warrant further investigation regarding their function. Our data provide a foundation for future investigations of hindgut bacterial factors that may influence the development and progression of chronic laminitis.

Effects of cereal β-glucans and enzyme inclusion on the porcine gastrointestinal tract microbiota

This study was designed to evaluate the effect barley-based diets vs. oats based diets on levels of Lactobacillus, Bifidobacterium and Enterobacterium in the porcine gastrointestinal tract (GIT). In addition the effect of enzyme supplementation in both diets was explored. Twenty-eight boars were used in a 2 × 2 factorial arrangement and were assigned to 1 of 4 dietary treatments: barley-based (B) diet; barley-based diet plus an enzyme supplement (B + ES); oat-based (O) diet or oat-based diet plus an enzyme supplement (O + ES). The enzyme supplement contained endo-1,3-β-glucanase and endo-1,4-β-xylanase. Faecal samples were collected from the pigs prior to initiations of the experiment and at slaughter. At slaughter digesta samples were collected from the stomach, ileum, caecum, proximal and distal colon. Alterations in Lactobacillus species composition in the gastrointestinal tract (GIT) were analysed by genus-specific PCR - denaturing gradient gel electrophoresis (DGGE). DGGE profiles indicated that cereal source provoked shifts in Lactobacillus population. The most diverse populations of lactobacilli emerged after feeding the O diets. Enzymes inclusion altered the composition of Lactobacillus species prevalent throughout the GIT in animals fed the B diet, causing a shift in the dominant lactobacilli present in the caecum and proximal colon. No such effect was evident in animals fed the enzyme supplemented O + ES diet. Microbial plate counts revealed that the O diets gave rise to higher counts of Lactobacillus in the caecum and colon and Bifidobacterium counts in the ileum, caecum and colon than the B diets. The O diet caused a 2 log increase in Enterobacterium counts in the proximal colon, no such effects were observed in animals fed the B, the B + ES or the O + ES diets. Overall both O diets had a more positive influence on the counts of the beneficial microorganisms and richness of the Lactobacillus population in the porcine GIT.

A comparison of the microbiome and the metabolome of different regions of the equine hindgut

The microbiome and associated metabolome of faecal samples were compared to those from the caecum and right dorsal colon of horses and ponies euthanised for nonresearch purposes by investigating the microbial population community structure as well as their functional metabolic products. Through the use of 16S rRNA gene dendrograms, the caecum microbiome was shown to cluster separately from the other gut regions. 16S rRNA gene-based quantitative PCR (q-PCR) also demonstrated differences between the caecum and the other gut regions. Metabolites as identified by Fourier transform infrared clustered in a similar way and specific metabolic products (volatile fatty acids and ammonia) also varied by region. Protozoal 18S rDNA concentration and archaeal mcrA gene concentration quantified by q-PCR were found in higher numbers in the colon than the other gut regions. Diversity calculations using Simpson and Shannon-Wiener indices demonstrated higher diversity in the right dorsal colon and faeces than in the caecum. All findings of this study suggest that faecal samples are likely to represent the microbial population of the right dorsal colon to some extent but not that of the caecum, indicating careful consideration is required when planning microbial investigations of the hindgut of the horse.

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.

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

Foregut fermentation occurs in mammalian ruminants and in one bird, the South American folivorous hoatzin. This bird has an enlarged crop with a function analogous to the rumen, where foregut microbes degrade the otherwise indigestible plant matter, providing energy to the host from foregut fermentation, in addition to the fermentation that occurs in their hindguts (cecum/colon). As foregut fermentation represents an evolutionary convergence between hoatzins and ruminants, our aim was to compare the community structure of foregut and hindgut bacterial communities in the cow and hoatzin to evaluate the influences of host phylogeny and organ function in shaping the gut microbiome. The approach used was to hybridize amplified bacterial ribosomal RNA genes onto a high-density microarray (PhyloChip). The results show that the microbial communities cluster primarily by functional environment (foreguts cluster separately from hindguts) and then by host. Bacterial community diversity was higher in the cow than in the hoatzin. Overall, compared with hindguts, foreguts have higher proportions of Bacteroidetes and Spirochaetes, and lower proportions of Firmicutes and Proteobacteria. The main host differences in gut bacterial composition include a higher representation of Spirochaetes, Synergistetes and Verrucomicrobia in the cow. Despite the significant differences in host phylogeny, body size, physiology and diet, the function seems to shape the microbial communities involved in fermentation. Regardless of the independent origin of foregut fermentation in birds and mammals, organ function has led to convergence of the microbial community structure in phylogenetically distant hosts.

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.

Cadmium chloride exhibits a profound toxic effect on bacterial microflora of the mice gastrointestinal tract

Cadmium (Cd²(+)), a naturally occurring heavy metal, is an important environmental pollutant and a potent toxicant to bacteria. The gastrointestinal (GI) tract microflora has a marked capacity to cope with the increased load of ingested metals. However, heavy metals may have harmful effects on GIT microflora. Under the conditions of experimental exposure to cadmium, changes in the population of intestinal microflora in healthy mice were examined. Five experimental groups received 23 to 50 mg kg⁻¹ cadmium in drinking water and control group was given water free from cadmium for 45 days. Intestinal contents and biopsy samples were aseptically collected and bacterial counts were performed. The microflora of the intestine in control group was represented by bacteria of the genera Bacillus cereus, Lactobacillus spp., Clostridium spp., Escherichia coli, Klebsiella spp., Pseudomonas spp., Enterococcus spp. and Proteus spp. As the result of dysbiosis induced by the introduction of cadmium, a sharp decrease in the population of all microbial species in the intestine was observed. The deleterious effect of cadmium appeared to be less in the large intestine and rectum than that of small intestine, suggesting a site-specific influence of cadmium. The gram-negative bacteria tested were less sensitive to cadmium compared to the gram-positive bacteria because of their possible different ability to uptake the metal ions.

The bacterial community of the horse gastrointestinal tract and its relation to fermentative acidosis, laminitis, colic, and stomach ulcers

The gastrointestinal tract of the horse has unique characteristics that make it well suited for the ingestion and utilization of roughage. The horse is considered a simple-stomached herbivore and is classed as a hindgut fermenter. The upper segments of the gastrointestinal tract resemble those of a typical simple-stomached animal. The lower have undergone modification to become voluminous and host to a large number of microbial populations similar to those of the compartmental stomach of ruminant animals. The main advantage of this arrangement is the ability of the horse to extract valuable nutrients from the diet before digesta reaches the hindgut where the rigid structural components that resisted enzymatic digestion at the small intestinal level undergo extensive fermentation processes.

Effects on the equine colon ecosystem of grass silage and haylage diets after an abrupt change from hay

The objective of this study was to investigate the effect of an abrupt change from grass hay (81% DM) to grass silage (36% DM) or grass haylage (55% DM), fed at similar DM intakes, and to compare the effects of silage and haylage on the composition and activities of the colon microflora. The forages were from the same swath harvested on the same day. Four adult colon-fistulated geldings were randomly assigned to diets in a crossover design. The study started with a preperiod when all 4 horses received the hay diet, followed by an abrupt feed change to the haylage diet for 2 horses and the silage diet for 2 horses. All 4 horses then had a new second preperiod of hay, followed by an abrupt feed change to the opposite haylage and silage diet. The periods were 21 d long, and the forage-only diets were supplemented with minerals and salt. The abrupt feed changes were made at 0800 h. Colon samples were taken before the abrupt feed change, 4 and 28 h after the feed change, and 8, 15, and 21 d after the feed change, all at 1200 h. Colon bacterial counts, VFA, pH, and DM concentrations were unchanged throughout the first 28 h after the abrupt feed change from hay to haylage and silage. Also, fecal pH and DM concentrations were unchanged during the first 28 h. During the weekly observations, colon lactobacilli counts increased (P = 0.023) in horses receiving the silage diet and were greater than on the haylage diet at 21 d. Streptococci counts decreased (P = 0.046) in horses receiving the haylage diet and were less than on the silage diet at 15 and 21 d. Total VFA concentrations and colon and fecal pH did not differ between diets and were unchanged throughout the weekly observations. The DM concentration of colon digesta and feces decreased (P = 0.030 and 0.049, respectively) on both diets during the weekly observations. The results suggest that in horses fed at the maintenance level of energy intake, an abrupt feed change from grass hay to grass silage or grass haylage from the same crop does not induce any major alterations in the colon ecosystem during the first 28 h. During the subsequent 3-wk period, colon and fecal DM decreased and there were alterations in the lactobacilli and streptococci bacterial counts. The changes in lactobacilli and streptococci counts need further investigation.