Daily intake of baru (Dipteryx alata Vog.), a Cerrado native almond, promotes changes in the intestinal microbiota of individuals with obesity: A pilot study.

The Brazilian Cerrado biome is rich in plant biodiversity, with fruits that have unique sensory characteristics and high nutritional quality. Among the various fruits, baru (Dipteryx alata Vog.) has attracted the attention of researchers because of its high lipid, protein, carbohydrate, fiber, and micronutrient (minerals and vitamins) contents. The present study evaluated the effects of regular consumption of baru almonds for over 60 days on the biochemical and anthropometric profiles and fecal microbiota of obese individuals. A pilot study was conducted on 15 individuals with obesity who were instructed to consume a 20-gram portion of baru almonds throughout the day. The body composition was assessed using anthropometric measurements. Blood pressure, glucose levels, lipid profile, serum insulin and iron contents, and fecal microbiota composition were determined at baseline (day 0) and after 60 days. Baru almond consumption contributed to changes in biochemical parameters, improved HDL cholesterol levels, and reduced total and LDL cholesterol levels. Some positive changes in the microbiota composition after consuming baru almonds include a decrease in the Faecalibacterium family and an increase in the Provotella genus. Therefore, ingesting baru almonds can modulate gut microbiota of individuals with obesity.

A Two-Step Single Plex PCR Method for Evaluating Key Colonic Microbiota Markers in Young Mexicans with Autism Spectrum Disorders: Protocol and Pilot Epidemiological Application.

Many neurological disorders have a distinctive colonic microbiome (CM) signature. Particularly, children with autism spectrum disorders (ASD) exhibit a very dissimilar CM when compared to neurotypical (NT) ones, mostly at the species level. Thus far, knowledge on this matter comes from high-throughput (yet very expensive and time-consuming) analytical platforms, such as massive high-throughput sequencing of bacterial 16S rRNA. Here, pure (260/280 nm, ~1.85) stool DNA samples (200 ng.µL-1) from 48 participants [39 ASD, 9 NT; 3-13 y] were used to amplify four candidate differential CM markers [Bacteroides fragilis (BF), Faecalibacterium prausnitzii (FP), Desulfovibrio vulgaris (DV), Akkermansia muciniphila (AM)], using micro-organism-specific oligonucleotide primers [265 bp (BF), 198 bp (FP), 196 bp (DV), 327 bp (AM)] and a standardized two-step [low (step 1: °Tm-5 °C) to high (stage 2: °Tm-0 °C) astringent annealing] PCR protocol (2S-PCR). The method was sensitive enough to differentiate all CM biomarkers in the studied stool donors [↑ abundance: NT (BF, FP, AM), ASD (DV)], and phylogenetic analysis confirmed the primers' specificity.

Impact of Saccharomyces boulardii CNCM I-745 on Bacterial Overgrowth and Composition of Intestinal Microbiota in Diarrhea-Predominant Irritable Bowel Syndrome Patients: Results of a Randomized Pilot Study.

BACKGROUND: Small intestinal bacterial overgrowth (SIBO) is associated with diarrhea-predominant irritable bowel syndrome (IBS-D). Probiotics like Saccharomyces boulardii CNCM I-745 (Sb) may be efficacious in balancing the microbiota. This randomized open label study assessed the effect of Sb in patients with bacterial overgrowth associated with IBS-D and its impact on the intestinal microbiota. METHODS: Patients were randomized to receive Sb + dietary advice (Sb + DA) or dietary advice (DA) only for 15 days. SIBO was assessed by the lactulose hydrogen breath test (LHBT). Symptoms were assessed with the IBS Symptom Severity Scale (IBS-SSS) and stool consistency with the Bristol Stool Form Scale. Microbiota and mycobiota were analyzed by 16S rDNA and ITS2. RESULTS: 54 patients were included, among whom 48 (27 Sb + DA, 21 DA) were evaluated. Decrease of hydrogen excretion was slightly higher in Sb + DA group, 41% versus 29% in DA group, and IBS-SSS total score were reduced by -134 and -93, respectively. The proportion of patients with diarrhea was lower in the Sb + DA group than in the DA group (25.9% compared to 47.6%). Bacterial and fungal microbiota showed that Sb treatment was associated with several modifications. Interestingly, F. prausnitzii was more abundant in Sb-treated patients with marked clinical improvement. The safety of S. boulardii CNCM I-745 was excellent. CONCLUSIONS: In patients with SIBO, S. boulardii CNCM I-745 associated with dietary advice reduced bacterial overgrowth and improved digestive symptoms while restoring the intestinal microbiota. The increased abundance of F. prausnitzii coupled with symptom improvement merits further research.

Metagenomics analysis reveals universal signatures of the intestinal microbiota in colorectal cancer, regardless of regional differences

The human gut microbiota is a complex and dynamic community of microorganisms living in our intestines and has emerged as an important factor for colorectal adenocarcinoma (CRC). The purpose of our study was to investigate the microbiota composition in Brazilian CRC patients compared with a local control population (CTL) to find out which changes could be considered universal or regional features in CRC microbiota. Fecal samples were obtained from 28 CRC and 23 CTL individuals. The 16S rRNA gene was used for metagenomic analysis. In addition to the anthropometric variables, the clinical stage (TNM 2018) was considered. Patients with CRC had a significant increase in alpha diversity and a higher percentage of genus Prevotella and a decreased proportion of Megamonas and Ruminococcus. Additionally, the proportion of Faecalibacterium prausnitzii was associated with a better prognosis in the first stages of CRC, and Fusobacterium nucleatum proved to be an important marker of colorectal carcinogenesis and tumor aggressiveness. Although regional differences influence the composition of the microbiota, in the case of CRC, the microhabitat created by the tumor seems to be a major factor. Our results contribute to a better understanding of the carcinogenic process, and even in different environments, some factors appear to be characteristic of the microbiota of patients with CRC.

Possible Benefits of Faecalibacterium prausnitzii for Obesity-Associated Gut Disorders.

Metabolic disorders are an increasing concern in the industrialized world. Current research has shown a direct link between the composition of the gut microbiota and the pathogenesis of obesity and diabetes. In only a few weeks, an obesity-inducing diet can lead to increased gut permeability and microbial dysbiosis, which contributes to chronic inflammation in the gut and adipose tissues, and to the development of insulin resistance. In this review, we examine the interplay between gut inflammation, insulin resistance, and the gut microbiota, and discuss how some probiotic species can be used to modulate gut homeostasis. We focus primarily on Faecalibacterium prausnitzii, a highly abundant butyrate-producing bacterium that has been proposed both as a biomarker for the development of different gut pathologies and as a potential treatment due to its production of anti-inflammatory metabolites.

A higher bacterial inward BCAA transport driven by Faecalibacterium prausnitzii is associated with lower serum levels of BCAA in early adolescents.

BACKGROUND: Elevations of circulating branched-chain amino acids (BCAA) are observed in humans with obesity and metabolic comorbidities, such as insulin resistance. Although it has been described that microbial metabolism contributes to the circulating pool of these amino acids, studies are still scarce, particularly in pediatric populations. Thus, we aimed to explore whether in early adolescents, gut microbiome was associated to circulating BCAA and in this way to insulin resistance. METHODS: Shotgun sequencing was performed in DNA from fecal samples of 23 early adolescents (10-12 years old) and amino acid targeted metabolomics analysis was performed by LC-MS/MS in serum samples. By using the HUMAnN2 algorithm we explored microbiome functional profiles to identify whether bacterial metabolism contributed to serum BCAA levels and insulin resistance markers. RESULTS: We identified that abundance of genes encoding bacterial BCAA inward transporters were negatively correlated with circulating BCAA and HOMA-IR (P < 0.01). Interestingly, Faecalibacterium prausnitzii contributed to approximately ~ 70% of bacterial BCAA transporters gene count. Moreover, Faecalibacterium prausnitzii abundance was also negatively correlated with circulating BCAA (P = 0.001) and with HOMA-IR (P = 0.018), after adjusting for age, sex and body adiposity. Finally, the association between Faecalibacterium genus and BCAA levels was replicated over an extended data set (N = 124). CONCLUSIONS: We provide evidence that gut bacterial BCAA transport genes, mainly encoded by Faecalibacterium prausnitzii, are associated with lower circulating BCAA and lower insulin resistance. Based on the later, we propose that the relationship between Faecalibacterium prausnitzii and insulin resistance, could be through modulation of BCAA.

Avaliação da microbiota intestinal em adultos com esofagite erosiva / Assessment of the intestinal microbiota in adults with erosive esophagitis

ABSTRACT BACKGROUND: The intestinal microbiota influences the appropriate function of the gastrointestinal tract. Intestinal dysbiosis may be associated with a higher risk of esophageal lesions, mainly due to changes in gastroesophageal motility patterns, elevation of intra-abdominal pressure, and increased frequency of transient relaxation of the lower esophageal sphincter. OBJECTIVE: The aim of this study was to evaluate the intestinal microbiota in individuals with erosive esophagitis and in healthy individuals using metagenomics. METHODS: A total of 22 fecal samples from adults aged between 18 and 60 years were included. Eleven individuals had esophagitis (eight men and three women) and 11 were healthy controls (10 men and one woman). The individuals were instructed to collect and store fecal material into a tube containing guanidine solution. The DNA of the microbiota was extracted from each fecal samples and PCR amplification was performed using primers for the V4 region of the 16S rRNA gene. The amplicons were sequenced using the Ion Torrent PGM platform and the data were analyzed using the QIIME™ software version 1.8. Statistical analyses were performed using the Mann-Whitney non-parametric test and the ANOSIM non-parametric method based on distance matrix. RESULTS: The alpha-diversity and beta-diversity indices were similar between the two groups, without statistically significant differences. There was no statistically significant difference in the phylum level. However, a statistically significant difference was observed in the abundance of the family Clostridiaceae (0.3% vs 2.0%, P=0.032) and in the genus Faecaliumbacterium (10.5% vs 4.5%, P=0.045) between healthy controls and esophagitis patients. CONCLUSION: The findings suggest that reduced abundance of the genus Faecaliumbacterium and greater abundance of the family Clostridiaceae may be risk factors for the development of erosive esophagitis. Intervention in the composition of the intestinal microbiota should be considered as an adjunct to current therapeutic strategies for this clinical condition.

RESUMO CONTEXTO: A doença do refluxo gastroesofágico (DRGE) é uma das enfermidades mais comuns na prática clínica e possui fisiopatologia multifatorial. Disbiose da microbiota intestinal pode ter influência em mecanismos envolvidos nesta doença, como mudanças nos padrões motores gastrointestinais, elevação da pressão intra-abdominal e aumento da frequência de relaxamentos transitórios do esfíncter esofágico inferior. Contudo, a avaliação da microbiota intestinal, neste contexto, ainda é pouco documentada. OBJETIVO: Este estudo avaliou a microbiota bacteriana intestinal, em indivíduos com doença do refluxo gastroesofágico erosivo e em indivíduos saudáveis, utilizando técnicas de metagenômica. MÉTODOS: Estudo incluiu amostras fecais de 22 adultos, com idades entre 18 e 60 anos: 11 com esofagite erosiva (oito homens e três mulheres) e 11 controles saudáveis (dez homens e uma mulher). Os pacientes foram orientados a coletar e armazenar o material fecal em tubo contendo solução de guanidina. O DNA da microbiota foi extraído das amostras de fezes e amplificação por PCR foi realizada usando iniciadores para a região V4 do gene 16S rRNA. Os amplicons foram seqüenciados usando a plataforma Ion PGM Torrent e os dados foram analisados usando o software QIIME™ versão 1.8 (Quantitative Insights Into Microbial Ecology). Análise de estatística foi realizada utilizando-se o teste não paramétrico de Mann-Whitney e o teste ANOSIM, método não paramétrico baseado em matriz de distância. RESULTADOS: Os índices de alfa-diversidade e beta-diversidade foram semelhantes entre os dois grupos, sem diferença estatisticamente significante. Não houve diferença estatisticamente significante no nível de filo, classe e ordem. Entretanto, observou-se diferença estatisticamente significante na abundância da família Clostridiaceae (0,3% vs 2,0%, P=0,032) e no gênero Faecaliumbacterium (10,5% vs 4,5%, P=0,045) entre controles saudáveis e pacientes com DRGE erosiva, respectivamente. CONCLUSÃO: Os achados sugerem que menor abundância do gênero Faecaliumbacterium e maior abundância da família Clostridiaceae, nos pacientes com DRGE, podem influenciar na fisiopatologia desta doença.

Effect of dietary inclusion of dried apple pomace on faecal butyrate concentration and modulation of gut microbiota in dogs.

This research aimed to evaluate the apparent total tract digestibility (ATTD) of nutrients, metabolisable energy (ME) and palatability of the diet, as well as products of intestinal fermentation and faecal microbiota of dogs fed with dried apple. For this purpose, three experiments were performed. In Experiment I, digestibility and ME of four diets containing 0%, 3%, 6% and 9% dried apple were evaluated, in addition to the faecal characteristics of the dogs. The diets were offered to eight adult dogs, distributed in double Latin square (4 × 4), totalling eight repetitions per treatment. In Experiment II, products of intestinal fermentation and faecal microbiota from 16 adult dogs fed diets containing 0% and 9% dried apple for 30 d (n = 8) were evaluated. Finally, Experiment III compared the dietary preference of 0 vs. 9% dried apple using 15 adult dogs. The inclusion of dried apple in the diet (p < 0.05) showed a linear reduction in the ATTD of dry matter (DM), crude protein (CP), and acid hydrolysed ether extract (EEA), and a linear increase in the ATTD of total dietary fibre (TDF). Consumption of 9% of dried apple increased faecal butyrate and reduced propionate and ammonia (p < 0.05). With this diet, there was also an increase (p < 0.05) in the faecal concentration of Faecalibacterium, Erysipelatoclostridium, Blautia, and Bacteroides. No differences were found in the palatability of the diets. The inclusion of up to 9% of dried apple in the diet reduces the digestibility of nutrients and does not influence the dogs' food preference; however, it improves some indicators of dogs' intestinal functionality.

Effects of gastrointestinal digested polyphenolic enriched extracts of Chilean currants (Ribes magellanicum and Ribes punctatum) on in vitro fecal microbiota.

Chilean currants (Ribes magellanicum and Ribes punctatum) are wild polyphenol-rich berries with interesting bioactivities in several in vitro models. The aim of this study was to investigate the effects of the pre-digested PEE (polyphenol-enriched extract) in a simulated colon model. Fruits were extracted, submitted to simulated gastrointestinal digestion and further colonic fermentation with feces from healthy human donors. Samples were taken at 1, 4, 8 and 24 h of incubation, monitoring pH, ammonia, branched-chain fatty acids (BCFA), short-chain fatty acids (SCFA) and bacterial growth. FOS (fructooligosaccharides) and fecal slurry without treatments were positive and negative control, respectively. Both Ribes species reduced (p < 0.05) both BCFA and SCFA at 24 h. R. punctatum promoted the growth (p < 0.05) of beneficial bacteria such as Clostridium cluster XIVa, and Faecalibacterium prausnitzii; while a trend to increase Akkermansia muciniphila was observed. R. magellanicum increased (p < 0.05) Clostridium cluster XIVa population. Escherichia coli, Lactobacillus spp. and Bifidobacterium spp. remained unaffected. Our results suggest that polyphenols from R. punctatum and R. magellanicum may modulate both bacterial metabolism and some selected gut beneficial bacteria under simulated conditions. Therefore, Chilean currants might be useful as supplements to maintain a healthy colon; however, further in vivo studies are needed to confirm their effect and their mechanisms.

New Insights into the Diversity of the Genus Faecalibacterium.

Faecalibacterium prausnitzii is a commensal bacterium, ubiquitous in the gastrointestinal tracts of animals and humans. This species is a functionally important member of the microbiota and studies suggest it has an impact on the physiology and health of the host. F. prausnitzii is the only identified species in the genus Faecalibacterium, but a recent study clustered strains of this species in two different phylogroups. Here, we propose the existence of distinct species in this genus through the use of comparative genomics. Briefly, we performed analyses of 16S rRNA gene phylogeny, phylogenomics, whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome to better elucidate the phylogenetic relationships among strains of Faecalibacterium. For this, we used 12 newly sequenced, assembled, and curated genomes of F. prausnitzii, which were isolated from feces of healthy volunteers from France and Australia, and combined these with published data from 5 strains downloaded from public databases. The phylogenetic analysis of the 16S rRNA sequences, together with the wgMLST profiles and a phylogenomic tree based on comparisons of genome similarity, all supported the clustering of Faecalibacterium strains in different genospecies. Additionally, the global analysis of gene synteny among all strains showed a highly fragmented profile, whereas the intra-cluster analyses revealed larger and more conserved collinear blocks. Finally, ANI analysis substantiated the presence of three distinct clusters-A, B, and C-composed of five, four, and four strains, respectively. The pangenome analysis of each cluster corroborated the classification of these clusters into three distinct species, each containing less variability than that found within the global pangenome of all strains. Here, we propose that comparison of pangenome subsets and their associated α values may be used as an alternative approach, together with ANI, in the in silico classification of new species. Altogether, our results provide evidence not only for the reconsideration of the phylogenetic and genomic relatedness among strains currently assigned to F. prausnitzii, but also the need for lineage (strain-based) differentiation of this taxon to better define how specific members might be associated with positive or negative host interactions.

Crohn associated microbial communities associated to colonic mucosal biopsies in patients of the western Mediterranean.

Next generation sequencing approaches allow the retrieval of several orders of magnitude larger numbers of amplified single sequences in 16S rRNA diversity surveys than classical methods. However, the sequences are only partial and thus lack sufficient resolution for a reliable identification. The OPU approach used here, based on a tandem combination of high quality 454 sequences (mean >500 nuc) applying strict OTU thresholds, and phylogenetic inference based on parsimony additions to preexisting trees, seemed to improve the identification yields at the species and genus levels. A total of thirteen biopsies of Crohn-diagnosed patients (CD) and seven healthy controls (HC) were studied. In most of the cases (73%), sequences were affiliated to known species or genera and distinct microbial patterns could be distinguished among the CD subjects, with a common depletion of Clostridia and either an increased presence of Bacteroidetes (CD1) or an anomalous overrepresentation of Proteobacteria (CD2). Faecalibacterium prausnitzii presence was undetectable in CD, whereas Bacteroides vulgatus-B. dorei characterized HC and some CD groups. Altogether, the results showed that a microbial composition with predominance of Clostridia followed by Bacteroidetes, with F. prausnitzii and B. vulgatus-B. dorei as major key bacteria, characterized what could be considered a balanced structure in HC. The depletion of Clostridia seemed to be a common trait in CD.