Firmicutes/Bacteroidetes and Firmicutes/Proteobacteria ratios are associated with worse prognosis in a cohort of Latin American patients with cirrhosis.

BACKGROUND: Some evidence suggests an association between gut dysbiosis and cirrhosis progression. The authors investigated Gut Microbiome (GM) influence on 90-day mortality and hospitalization/rehospitalization rates in cirrhotic patients. METHODS: Compensated/decompensated outpatients and decompensated inpatients were prospectively included and compared to healthy controls. Clinical, laboratory, GM, and two ratios between phyla were evaluated. Patients were followed up for 90 days for hospitalization/rehospitalization and mortality. RESULTS: 165 individuals were included (50 compensated, 49 decompensated outpatients; 36 decompensated inpatients; 30 healthy), 48.5 % female, mean age was 61, main cirrhosis etiology was hepatitis C (27.3 %), and mostly Child-Pugh (CP) B patients, median MELD of 13. As liver disease progressed, microbiota diversity decreased between the groups (p = 0.05; p < 0.004). There were 9 deaths and 22 hospitalizations or rehospitalizations. GM composition had correlation with norfloxacin (p = 0.36, p = 0.04), encephalopathy (p = 0.31, p = 0.01), lactulose (p = 0.26, p = 0.01), 90-day mortality (p = 0.22, p = 0.04), CP (p = 0.17, p = 0.01), previous 6-month antibiotic use (p = 0.16, p = 0.01), MELD (p = 0.145, p = 0.01), ALBI (p = 0.1, p = 0.04) and 90-day hospitalization/rehospitalization (p = 0.08, p = 0.03). Firmicutes/Bacteroidetes (F/B) and Firmicutes/Proteobacteria (F/P) ratios were progressively lower and more significant and had an association with 90-day mortality (p < 0.001). Three MELD set-points (≥ 15, 18 and 20) were significantly associated with both ratios, with similar accuracies. CONCLUSIONS: GM dysbiosis was associated with higher CP, MELD, 90-day mortality and hospitalization/rehospitalization. F/B and F/P ratios were associated with 90-day mortality.

Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight.

This study examined the interplay between bacterial and fungal communities in the human gut microbiota, impacting on nutritional status and body weight. Cohorts of 10 participants of healthy weight, 10 overweight, and 10 obese individuals, underwent comprehensive analysis, including dietary, anthropometric, and biochemical evaluations. Microbial composition was studied via gene sequencing of 16S and ITS rDNA regions, revealing bacterial (bacteriota) and fungal (mycobiota) profiles. Bacterial diversity exceeded fungal diversity. Statistically significant differences in bacterial communities were found within healthy-weight, overweight, and obese groups. The Bacillota/Bacteroidota ratio (previously known as the Firmicutes/Bacteroidetes ratio) correlated positively with body mass index. The predominant fungal phyla were Ascomycota and Basidiomycota, with the genera Nakaseomyces, Kazachstania, Kluyveromyces, and Hanseniaspora, inversely correlating with weight gain; while Saccharomyces, Debaryomyces, and Pichia correlated positively with body mass index. Overweight and obese individuals who harbored a higher abundance of Akkermansia muciniphila, demonstrated a favorable lipid and glucose profiles in contrast to those with lower abundance. The overweight group had elevated Candida, positively linked to simple carbohydrate consumption. The study underscores the role of microbial taxa in body mass index and metabolic health. An imbalanced gut bacteriota/mycobiota may contribute to obesity/metabolic disorders, highlighting the significance of investigating both communities.

Tartrate fermentation with H2 production by a new member of Sporomusaceae enriched from rice paddy soil.

In rice paddies, soil and plant-derived organic matter are degraded anaerobically to methane (CH4), a powerful greenhouse gas. The highest rate of methane emission occurs during the reproductive stage of the plant when mostly dicarboxylic acids are exudated by the roots. The emission of methane at this stage depends largely on the cooperative interaction between dicarboxylic acid-fermenting bacteria and methanogenic archaea in the rhizosphere. The fermentation of tartrate, one of the major acids exudated, has been scarcely explored in rice paddy soils. In this work, we characterized an anaerobic consortium from rice paddy soil composed of four bacterial strains, whose principal member (LT8) can ferment tartrate, producing H2 and acetate. Tartrate fermentation was accelerated by co-inoculation with a hydrogenotrophic methanogen. The assembled genome of LT8 possesses a Na+-dependent oxaloacetate decarboxylase and shows that this bacterium likely invests part of the H2 produced to reduce NAD(P)+ to assimilate C from tartrate. The phylogenetic analysis of the 16S rRNA gene, the genome-based classification as well as the average amino acid identity (AAI) indicated that LT8 belongs to a new genus within the Sporomusaceae family. LT8 shares a few common features with its closest relatives, for which tartrate degradation has not been described. LT8 is limited to a few environments but is more common in rice paddy soils, where it might contribute to methane emissions from root exudates.IMPORTANCEThis is the first report of the metabolic characterization of a new anaerobic bacterium able to degrade tartrate, a compound frequently associated with plants, but rare as a microbial metabolite. Tartrate fermentation by this bacterium can be coupled to methanogenesis in the rice rhizosphere where tartrate is mainly produced at the reproductive stage of the plant, when the maximum methane rate emission occurs. The interaction between secondary fermentative bacteria, such as LT8, and methanogens could represent a fundamental step in exploring mitigation strategies for methane emissions from rice fields. Possible strategies could include controlling the activity of these secondary fermentative bacteria or selecting plants whose exudates are more difficult to ferment.

Comparative genomics reveals probable adaptations for xylose use in Thermoanaerobacterium saccharolyticum.

Second-generation ethanol, a promising biofuel for reducing greenhouse gas emissions, faces challenges due to the inefficient metabolism of xylose, a pentose sugar. Overcoming this hurdle requires exploration of genes, pathways, and organisms capable of fermenting xylose. Thermoanaerobacterium saccharolyticum is an organism capable of naturally fermenting compounds of industrial interest, such as xylose, and understanding evolutionary adaptations may help to bring novel genes and information that can be used for industrial yeast, increasing production of current bio-platforms. This study presents a deep evolutionary study of members of the firmicutes clade, focusing on adaptations in Thermoanaerobacterium saccharolyticum that may be related to overall fermentation metabolism, especially for xylose fermentation. One highlight is the finding of positive selection on a xylose-binding protein of the xylFGH operon, close to the annotated sugar binding site, with this protein already being found to be expressed in xylose fermenting conditions in a previous study. Results from this study can serve as basis for searching for candidate genes to use in industrial strains or to improve Thermoanaerobacterium saccharolyticum as a new microbial cell factory, which may help to solve current problems found in the biofuels' industry.

Exploring the microbiome of two uterine sites in cows.

Bacterial communities in the mammalian reproductive system can be rich and diverse, differing in structure and quantity depending on location. In addition, its microbiome is associated with the state of health of this tract and reproductive success. This study evaluated the microbiome composition of the uterine body (UB) and uterine horn mucosa (UH) samples using 16S rRNA sequencing of samples extracted from cows in the Amazon region. It was observed that four main phyla were shared between the uterine sites: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Linear discriminant analysis effect size and heat tree analysis showed that members of Lachnospiraceae (NK3A20 group) and Oscillospiraceae were significantly more abundant in the UB than in UH. In addition, there are more unique genera in the UB than in the UH. A higher bacterial load in UB than in UH is expected because of the exposure to external factors of UB. However, comparing the site's communities through beta diversity did not generate well-defined clustering. Thus, it can be attributed to the closeness of the sites, which would make the niches similar ecologically and microbiologically. Therefore, this research provides knowledge to understand biomarkers in the prior reproduction period.

Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables.

Chile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 104 to 108 copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal-Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.

Microbial colonization dynamics of the postnatal digestive tract of Bos indicus calves.

The rumen and the jejunum of calves have distinct functional roles; the former is in the storage and fermentation of feed, and the latter is in transporting digesta to the ileum. It is unknown how nutrition changes the evolution of the microbiome of these organs after birth. We sequenced and characterized the entire microbiome of the rumen and the jejunum from Bos indicus calves of the Mexican Tropics to study their dynamics at Days 0, 7, 28, and 42 after birth. Operational taxonomic units (OTUs) belonging to 185 and 222 genera from 15 phylum were observed in the organs, respectively. The most abundant OTUs were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. We observed that proteobacterial species were outcompeted after the first week of life by Bacteroidetes and Firmicutes in the rumen and the jejunum, respectively. Moreover, Prevotella species were found to predominate in the rumen (36% of total OTUs), while the jejunum microbiome is composed of small proportions of several genera. Presumably, their high relative abundance assists in specialized functions and is more likely in fermentation since they are anaerobes. In summary, the rumen and the jejunum microbiomes were outcompeted by new microbiomes in a dynamic process that begins at birth.

Monitoring of a microbial community during bioaugmentation with hydrogenotrophic methanogens to improve methane yield of an anaerobic digestion process.

Methane production by microbial fermentation of municipal waste is a challenge for better yield processes. This work describes the characterization of a hydrogenotrophic methanogen microbial community used in a bioaugmentation procedure to improve the methane yield in a thermophilic anaerobic process, digesting the organic fraction of municipal solid waste. The performance of the bioaugmentation was assessed in terms of methane production and changes in the microbial community structure. The results showed that bioaugmentation slightly improved the cumulative methane yield (+ 4%) in comparison to the control, and its use led to an acceleration of the methanogenesis stage. We observed associated significant changes in the relative abundance of taxa and their interactions, using high throughput DNA sequencing of V3-16S rRNA gene libraries, where the abundance of the archaeal hydrogenotrophic genus Methanoculleus (class Methanomicrobia, phylum Euryarchaeota) and the bacterial order MBA08 (class Clostridia, phylum Firmicutes) were dominant. The relevant predicted metabolic pathways agreed with substrate degradation and the anaerobic methanogenic process. The purpose of the study was to evaluate the effect of the addition of hydrogenotrophic methanogens in the generation of methane, while treating organic waste through anaerobic digestion.

Binding Specificity of a Novel Cyclo/Maltodextrin-Binding Protein and Its Role in the Cyclodextrin ABC Importer System from Thermoanaerobacterales.

Extracellular synthesis of functional cyclodextrins (CDs) as intermediates of starch assimilation is a convenient microbial adaptation to sequester substrates, increase the half-life of the carbon source, carry bioactive compounds, and alleviate chemical toxicity through the formation of CD-guest complexes. Bacteria encoding the four steps of the carbohydrate metabolism pathway via cyclodextrins (CM-CD) actively internalize CDs across the microbial membrane via a putative type I ATP-dependent ABC sugar importer system, MdxEFG-(X/MsmX). While the first step of the CM-CD pathway encompasses extracellular starch-active cyclomaltodextrin glucanotransferases (CGTases) to synthesize linear dextrins and CDs, it is the ABC importer system in the second step that is the critical factor in determining which molecules from the CGTase activity will be internalized by the cell. Here, structure-function relationship studies of the cyclo/maltodextrin-binding protein MdxE of the MdxEFG-MsmX importer system from Thermoanaerobacter mathranii subsp. mathranii A3 are presented. Calorimetric and fluorescence studies of recombinant MdxE using linear dextrins and CDs showed that although MdxE binds linear dextrins and CDs with high affinity, the open-to-closed conformational change is solely observed after α- and ß-CD binding, suggesting that the CM-CD pathway from Thermoanaerobacterales is exclusive for cellular internalization of these molecules. Structural analysis of MdxE coupled with docking simulations showed an overall architecture typically found in sugar-binding proteins (SBPs) that comprised two N- and C-domains linked by three small hinge regions, including the conserved aromatic triad Tyr193/Trp269/Trp378 in the C-domain and Phe87 in the N-domain involved in CD recognition and stabilization. Structural bioinformatic analysis of the entire MdxFG-MsmX importer system provided further insights into the binding, internalization, and delivery mechanisms of CDs. Hence, while the MdxE-CD complex couples to the permease subunits MdxFG to deliver the CD into the transmembrane channel, the dimerization of the cytoplasmatic promiscuous ATPase MsmX triggers active transport into the cytoplasm. This research provides the first results on a novel thermofunctional SBP and its role in the internalization of CDs in extremely thermophilic bacteria.

Metataxonomic characterization of the microbial community involved in the production of biogas with microcrystalline cellulose in pilot and laboratory scale.

Biogas, produced in anaerobic digestion, is a sustainable alternative for generating energy from agro-industrial and municipal waste. Information from the microbiota active in the process expands the possibilities for technological innovation. In this study, taxonomic annotations, and functional prediction of the microbial community of the inoculum of two processes were carried out: an industrial unit (pilot-scale urban solid waste plant-IU) and a laboratory-scale reactor fed with swine and cattle waste (LS). The biochemical potential of biogas was obtained using tested inoculum with microcrystalline cellulose, obtaining 682 LN/kgVS (LSC-laboratory scale inoculum and microcrystalline cellulose), and 583 LN/kgVS (IUC-industrial unit inoculum and microcrystalline cellulose), which is equivalent to a recovery of 91.5% of total biogas to LSC. The phyla Synergistota and Firmicutes were more abundant in LS/LSC. In the IU/IUC (treatment of restaurant waste and customs seizures), there was a greater microbiological variety and a predominance of the Bacteroidota, Cloacimonadota, Firmicutes and Caldatribacteriota. The genus Methanosaeta predominated in the process, and it was possible to infer the genes (K01895, K00193 and K00625) related to acetoclastic pathway, as well as endoglucanases that are involved in the metabolism of cellulose (LSC). Terpenoids, polyketides, cofactors, and vitamin metabolism were higher in reactors that received different substrates (IU; IUC). The taxonomic and functional differences revealed the importance of determining the microbiota in the analysis of the potential of an inoculum, combined with the use of microcrystalline cellulose, which can provide optimization information in the production of clean energy.

Metagenomics analysis of the morphological aspects and bacterial composition of broiler feces.

In this descriptive study, we used metagenomics to analyze the relationship between the morphological aspects of chicken feces and its respective bacterial compositions. The microbiota composition was determined by sequencing the V4 region of the 16S rRNA genes collected from fresh broiler feces at 19 d old. In total, 48 samples were collected and divided into 8 groups of 6 samples each. The morphological changes studied were feed passage (FP) and reddish mucus (RM). Each was classified into 3 levels of intensity: 1 (slight), 2 (moderate), or 3 (intense). Thus, the 8 groups studied were feed passage (FP-1; FP-2; FP-3), reddish mucus (RM-1; RM-2; RM-3), normal ileal feces (NIF), and cecal discharge (CD). The alpha diversity (Shannon's index) revealed that the CD group showed greater diversity, and was significantly different from FP-2, FP-3, and RM-1. The beta diversity showed that the CD group samples were more homogeneous than the ileal feces groups. The relative abundance analysis revealed that Firmicutes and Proteobacteria were the most abundant phyla in the ileal feces groups. In CD, Firmicutes and Bacteroidetes were the most abundant. The relative abundance at the genus level revealed 136 different bacterial genera. In the ileal feces groups, the two most abundant genera were Lactobacillus and Escherichia/Shigella, except in the FP-1 and RM-2 groups, which had the opposite order. Unlike the others, the CD group had a higher abundance of Bacteroides and Faecalibacterium. When comparing the NIF group with the others, significant changes were found in the fecal microbiota, with nine genera for the FP groups, 19 for the RM groups, and 61 when compared to CD. The results of the present study suggest that evaluation of fecal morphology is a fundamental task that makes it possible to act quickly and assertively, as the morphological aspects of the feces may be related to the composition and structure of fecal microbiota.

The Entero-Mammary Pathway and Perinatal Transmission of Gut Microbiota and SARS-CoV-2.

COVID-19 is a severe respiratory disease threatening pregnant women, which increases the possibility of adverse pregnancy outcomes. Several recent studies have demonstrated the ability of SARS-CoV-2 to infect the mother enterocytes, disturbing the gut microbiota diversity. The aim of this study was to characterize the entero-mammary microbiota of women in the presence of the virus during delivery. Fifty mother−neonate pairs were included in a transversal descriptive work. The presence of SARS-CoV-2 RNA was detected in nasopharyngeal, mother rectal swabs (MRS) and neonate rectal swabs (NRS) collected from the pairs, and human colostrum (HC) samples collected from mothers. The microbiota diversity was characterized by high-throughput DNA sequencing of V3-16S rRNA gene libraries prepared from HC, MRS, and NRS. Data were analyzed with QIIME2 and R. Our results indicate that several bacterial taxa are highly abundant in MRS positive for SARS-CoV-2 RNA. These bacteria mostly belong to the Firmicutes phylum; for instance, the families Bifidobacteriaceae, Oscillospiraceae, and Microbacteriaceae have been previously associated with anti-inflammatory effects, which could explain the capability of women to overcome the infection. All samples, both positive and negative for SARS-CoV-2, featured a high abundance of the Firmicutes phylum. Further data analysis showed that nearly 20% of the bacterial diversity found in HC was also identified in MRS. Spearman correlation analysis highlighted that some genera of the Proteobacteria and Actinobacteria phyla were negatively correlated with MRS and NRS (p < 0.005). This study provides new insights into the gut microbiota of pregnant women and their potential association with a better outcome during SARS-CoV-2 infection.

The digestive tract sections of the sea cucumber Isostichopus badionotus reveal differences in composition, diversity, and functionality of the gut microbiota.

For the first time, this study analyses the composition and diversity of the gut microbiota of Isostichopus badionotus in captivity, using high-throughput 16S rRNA sequencing, and predicts the metagenomic functions of the microbiota. The results revealed a different composition of the gut microbiota for the foregut (FG) and midgut (MG) compared to the hindgut (HG), with a predominance of Proteobacteria, followed by Actinobacteria, Bacteroidetes, and Firmicutes. The FG and MG demonstrated a greater bacterial diversity compared to the HG. In addition, a complex network of interactions was observed at the genus level and identified some strains with probiotic and bioremediation potentials, such as Acinetobacter, Ruegeria, Streptococcus, Lactobacillus, Pseudomonas, Enterobacter, Aeromonas, Rhodopseudomonas, Agarivorans, Bacillus, Enterococcus, Micrococcus, Bifidobacterium, and Shewanella. Predicting metabolic pathways revealed that the bacterial composition in each section of the intestine participates in different physiological processes such as metabolism, genetic and environmental information processing, organismal systems, and cellular processes. Understanding and manipulating microbe--host-environment interactions and their associated functional capacity could substantially contribute to achieving more sustainable aquaculture systems for I. badionotus.

Firmicutes, Bacteroidetes and Actinobacteria in Human Milk and Maternal Adiposity.

The main objective was to explore the relationship between the microbiota of human milk and adiposity in Mexican mothers during the first lactation stage. METHODS: Seventy lactating women were included. Adiposity by anthropometric measurements and by bioelectric impedance was obtained. The donation of human milk was requested, from which bacterial DNA was extracted and qPCR of the 16S region was performed. The Mann-Whitney U test, Spearman and Pearson correlations, and multiple linear regressions models were also calculated. RESULTS: The median percentage of Bacteroidetes had a direct and significant correlation with normal adiposity, current BMI, waist circumference, and body fat percentage. The correlation with current BMI became significantly inverse in women with BMI ≥ 25. In women with normal BMI, the percentage of Actinobacteria showed a direct and significant correlation with current BMI, waist circumference, and percentage of body fat. Multiple linear regressions showed that pre-pregnancy BMI was the variable with the highest predictive value with the Bacteroidetes phyla in normal BMI and in BMI ≥ 25. CONCLUSIONS: the adiposity of the woman before pregnancy and during lactation would have an important effect on the abundance of Bacteroidetes and Actinobacteria in human milk.

Nature and Prevalence of Bacterial Taxa Persisting after Root Canal Chemomechanical Preparation in Permanent Teeth: A Systematic Review and Meta-analysis.

INTRODUCTION: Culture-independent molecular studies have shown a broad spectrum of bacterial taxa that persist after chemomechanical procedures (CMP). Therefore, this study systematically reviewed these reports to explore the prevalence of bacteria in post-instrumentation samples of root canals from permanent teeth, especially of as-yet-uncultivated/difficult-to-culture bacteria. METHODS: Electronic databases were searched from 2007 to January 2021. Clinical studies using culture-independent molecular methods to identify species-level taxa before and after CMP were included. Studies were critically appraised using the Joanna Briggs Institute Prevalence Critical Appraisal Checklist and the funnel plot analysis. The meta-analysis was performed on the prevalence of as-yet-uncultivated/difficult-to-culture bacterial taxa using RStudio. RESULTS: A total of 3781 titles were screened, but only 20 studies were included. The most frequent species in post-instrumentation samples were Streptococcus spp., Leptotrichia buccalis, Fusobacterium nucleatum, and Capnocytophaga ochracea. The detection frequency of some species increased after CMP, including mainly Firmicutes members such as streptococci, Enterococcus faecium, Selenomonas noxia, and Solobacterium moorei. The prevalence (confidence interval) of difficult-to-culture species was as follows: Dialister invisus, 17% (7%-29%); Solobacterium moorei, 14% (8%-23%); Bacteroidaceae [G-1] bacterium HMT 272, 13% (5%-23%); and Filifactor alocis, 11% (3%-23%). CONCLUSIONS: The prevalence of as-yet-uncultivated/difficult-to-culture bacterial taxa in post-instrumentation samples was low. The persistent species belonged mainly to the phylum Firmicutes, and streptococci were the major members. Future larger clinical studies on the composition of the whole bacterial community that persist after CMP are still necessary for a better understanding of bacterial interactions and their clinical significance in the treatment outcome.

Relationship Among Blastocystis, the Firmicutes/Bacteroidetes Ratio and Chronic Stress in Mexican University Students.

The role played by Blastocystis in humans has been a subject of discussion due to its intestinal effects and modifications in the intestinal microbiota. We aimed to analyze the relationship between Blastocystis subtypes ST1-4 and 7, the Firmicutes to Bacteroidetes ratio (F/B ratio) of fecal microbiota, and chronic stress in university students. This study had a cross-sectional design with a sample of 202 students. We analyzed fecal and hair samples, and stress inventories were applied to the students. The results showed a frequency of Blastocystis-colonized students of 52.97%. Regarding fecal microbiota, a median RAU of 0.801 for Firmicutes and 0.82 of Bacteroidetes were obtained, with an F/B ratio of 0.83. A low F/B ratio (66.04%) was more frequent in Blastocystis-colonized students, whereas a high F/B ratio (68.09%) (p = < 0.0001) was found in the Blastocystis-non-colonized. Only Blastocystis ST3 did not significantly correlate with a low F/B ratio (p = 0.290). The ST4 was associated with lower values of cortisol (p = 0.030), psychological stress (p = 0.040), and lower frequency of constipation (p = 0.010). Only two students with the ST1 had abdominal pain (p = 0.007). Our results suggest that colonization by Blastocystis subtypes can modify the intestinal microbiota due to a decreased ratio between the two most representative phyla (F/B). Also, the results of this study show that ST4 colonization is related to a lower level of chronic stress.

Fecal Microbiome Responses to Sudden Diet Change in Mangalarga Marchador horses.

Sudden changes in horses' diet have been previously associated with gastrointestinal disease. This study evaluated the effects of a sudden change of diet composed exclusively of Coastcross hay (CHD) to a complete extruded diet (CED) on the fecal microbiome of horses. A completely randomized design with repeated measurements was used. The study started with eight adult horses randomly split into group A, fed with CHD, and group B, fed with CED. After 34 days of diet adaptation, the diets were abruptly changed between the groups. Fecal samples were collected at 0, 24, and 96 hours after the diet change, and the pH and microbiome analyses of the feces were subsequently evaluated. Changing from CHD to CED reduced the alpha diversity 24 hours after the alteration, with a decrease in the relative abundance of Firmicutes and an increase of Bacteroidetes. Fecal pH decreased and the relative abundance of Verrucomicrobia increased 96 hours after changing the diets. The community structure was also different after 96 hours of diet change. In contrast, 24 hours after changing from CED to CHD reduced fecal pH and abundance of Synergistetes. After 96 hours, there was an increase in the alpha diversity, and the abundance of the phylum Lentisphaerae. Group B showed no changes in the community structure when its diet was changed. Concluding, diet composition influenced the response of the equine fecal microbiome to sudden dietary changes.

Characterization of microbial communities and predicted metabolic pathways in the uterus of healthy mares.

Background: Culture-independent techniques have made it possible to expand the knowledge about the composition of bacterial communities present in the healthy uterus and their role in health and disease, mainly in humans. However, in animals like mares, there is a dearth of information regarding this area. Aim: To narrow this knowledge gap, the objective of this study was to identify and characterize the composition and function of the uterine microbiome of a group of Chilean purebred mares (CPM), an equine breed with the oldest genealogical record in South America and an economical important reproductive industry. Methods: From uterine biopsy samples obtained during estrus, DNA extraction and targeted sequencing were performed to investigate the bacterial diversity and its probable metabolic function. Results: CPM biopsy samples were characterized by having a varied microbial composition, where the four most relatively abundant phyla were Proteobacteria (69.6%), Firmicutes (21.1%), Bacteroidetes (7.8%), and Actinobacteria (1.06%); which made up 99.6% of the total identified phyla. In contrast, Actinobacteria and Fusobacteria were the phyla not identified in all samples. Of a total of 59 genera identified across all samples, Staphylococcus was the most abundant genus with an average relative abundance of 18.88%, followed by Pseudomonas (17.9%), Escherichia/Shigella (10.42%), and Klebsiella (9.92%). Conclusion: These findings contribute to the knowledge of microbes' presence in the uterus, while future studies are required to demonstrate the role of these microorganisms in health and disease.

Prevalence of Blastocystis and its association with Firmicutes/Bacteroidetes ratio in clinically healthy and metabolically ill subjects.

BACKGROUND: Blastocystis is a typical anaerobic colon protist in humans with controversial pathogenicity and has relation with alterations in the intestinal microbiota composition (dysbiosis), whose eventual indicator is the Firmicutes/Bacteroidetes ratio (F/B ratio); this indicator is also linked to complications such as diabetes, obesity, or inflammatory bowel disease. The present study investigated the prevalence of Blastocystis and its association with Firmicutes/Bacteroidetes ratio in healthy and metabolic diseased subjects. METHODS: Fecal and blood samples were collected consecutively from 200 healthy subjects and 84 subjects with metabolic disease; Blastocystis and its most frequent subtypes were identified by end-point PCR and the two most representative phyla of the intestinal microbiota Firmicutes and Bacteroidetes by real-time PCR. RESULTS: The prevalence of Blastocystis in healthy subjects was 47.0, and 65.48% in subjects with metabolic disease; the most prevalent subtype in the total population was ST3 (28.38%), followed by ST1 (14.86%), ST4, ST5, and ST7 (each one of them with 14.19% respectively), and finally ST2 (8.78%). The low F/B ratio was associated with the prevalence of Blastocystis in the two cohorts FACSA (OR = 3.78 p < 0.05) and UNEME (OR = 4.29 p < 0.05). Regarding the subtype level, an association between the FACSA cohort ST1 and ST7 with low Firmicutes/Bacteroidetes ratio was found (OR = 3.99 and 5.44 p < 0.05, respectively). CONCLUSIONS: The evident predatory role of Blastocystis over Firmicutes phylum was observed in both cohorts since the abundance of bacterial group's Bacteroidetes increases in the groups colonized by this eukaryote and, therefore, may have a beneficial effect.

Firmicutes Dysbiosis After Chlorhexidine Prophylaxis in Healthy Patients Submitted to Impacted Lower Third Molar Extraction.

Prophylaxis with antiseptic and antibiotic therapy is common in impacted lower third molar surgeries, despite the lack of consensus among professionals and researchers in the indication for healthy patients. The aim of the present preliminary study was to verify the impact of prophylaxis therapy with antiseptic and antibiotic in healthy patients submitted to impacted lower third molar extraction, according to oral microorganism quantification. Eleven patients submitted to impacted lower third molar extraction, under prophylactic therapy with 0.12% chlorhexidine and amoxicillin in four experimental phases, were evaluated. Our results showed no significant reduction in total bacteria load, as well as in Bacteroidetes and C. albicans loads in the oral cavity, after prophylactic therapy with antiseptic and antibiotic. On the other hand, there was a significant difference between the Firmicutes levels across the follow-up, and this effect seems to be large (ηp²=0.94). Post-hoc test demonstrated that the levels of Firmicutes in T1 were higher than T0, T2, and T3, suggesting a microbiota dysbiosis, when 0.12% chlorhexidine use, which may be responsible for selection of antibiotic-resistant microorganisms. Our results alert for an overuse of antiseptic and antibiotics by dentists and for a better evaluation of the available protocols.