A Possible Perspective about the Compositional Models, Evolution, and Clinical Meaning of Human Enterotypes

Among the various parameters obtainable through the analysis of the human gut microbiota, the enterotype is one of the first classifications of the bacterial consortia, which tried to obtain, at the same time, as much information as possible to be applied in clinical medicine. Although some authors observed the existence not of clusters, but only of a real continuous gradient, enterotypes are commonly described according to various models. The first model predicted either clustering into enterotypes 1 and 2 based on two specific dominances, Bacteroides and Prevotella, respectively, with the Ruminococcus dominance blurred within the Bacteroides dominance, or it predicted a threedominant condition, in which the Ruminococcus driver constituted enterotype 3, separated from enterotype 1. A second model envisaged three possible ways to cluster gut microbiota, respectively centred on two, three, and four dominances. In the first case, enterotypes 1 and 2 coincided with the two original enterotypes, with the dominance of Bacteroides and Prevotella, respectively. In the second case, the existence of enterotype 3 was evident and whose dominance was not centred on Ruminococcus but extended more towards the entire Firmicutes phylum. In the third case, the presence of the phylum Firmicutes was split into two different enterotypes generating the clusters defined and named as Mixtures 1 and 2. Subsequently, the analysis of the water content (hydration) in the stool allowed the splitting of the Bacteroides enterotype into two sub-enterotype, respectively known as B1 and B2. All these models have allowed us to highlight some correlations between a specific enterotype, or cluster, and some characteristics, such as the greater predisposition of the respective hosts towards certain pathologies. These observations, coupled with the attempt to derive the different microbiota on an evolutionary basis, can help to shed new light on this topic and demonstrate the possible utility that the different ways of clustering the gut microbiota can have in a clinical application perspective and in preventive medicine.

Effects of Dietary Glucose Oxidase Supplementation on the Performance, Apparent Ileal Amino Acids Digestibility, and Ileal Microbiota of Broiler Chickens

This study aimed to investigate the effects of glucose oxidase (GOD) supplementation on growth performance, apparent ileal digestibility (AID) of nutrients, intestinal morphology, and short-chain fatty acids (SCFAs) and microbiota in the ileum of broilers. Six hundred 1-day-old male broilers were randomly allotted to four groups of 10 replicates each with 15 birds per replicate cage. The four treatments included the basal diet without antibiotics (Control) and the basal diet supplemented with 250, 500, or 1000 U GOD/kg diet (E250, E500 or E1000). The samples of different intestinal segments, ileal mucosa, and ileal digesta were collected on d 42. Dietary GOD supplementation did not affect daily bodyweight gain (DBWG) and the ratio of feed consumption and bodyweight gain (FCR) during d 1-21 (p > 0.05); however, the E250 treatment increased DBWG (p = 0.03) during d 22–42 as compared to control. Dietary GOD supplementation increased the AIDs of arginine, isoleucine, lysine, methionine, threonine, cysteine, serine, and tyrosine (p < 0.05), while no significant difference was observed among the GOD added groups. The E250 treatment increased the villus height of the jejunum and ileum. The concentrations of secreted immunoglobulin A (sIgA) in ileal mucosa and the contents of acetic acid and butyric acid in ileal digesta were higher in the E250 group than in the control (p < 0.05), whereas no significant differences among E500, E1000, and control groups. The E250 treatment increased the richness of ileal microbiota, but E500 and E100 treatment did not significantly affect it. Dietary E250 treatment increased the relative abundance of Firmicutes phylum and Lactobacillus genus, while it decreased the relative abundance of genus Escherichina-Shigella (p < 0.05). Phylum Fusobacteria only colonized in the ileal digesta of E500 treated broilers and E500 and E1000 did not affect the relative abundance of Firmicutes phylum and Lactobacillus and Escherichina-Shigella genera as compared to control. These results suggested that dietary supplementation of 250 U GOD/kg diet improves the growth performance of broilers during d 22–42, which might be associated with the alteration of the intestinal morphology, SCFAs composition, and ileal microbiota composition.

DNA Metabarcoding of the Leachate Microbiota from Sanitary Landfill: potential for bioremediation process

Microbial profile knowledge is essential to news alternatives and improvements in current treatments and destinations of landfill leachate that contains a variety of toxic compounds produced by municipal solid waste (MSW) disposal. Environmental DNA metabarcoding is an efficient, quick, and low-cost methodology for whole communities’ characterization. In this respect, the leachate from the Sanitary Landfill of Foz do Iguaçu City showed mixed characteristics from both acid and methanogenic phases, and 16S rDNA metabarcoding suggested the dominance of fermenting bacteria belonging to Firmicutes phylum, followed by Proteobacteria, Bacteroidetes and Synergistetes. The leachate acidogenic phase ended up being masked in the chemical and physical analyzes, however was evidenced in the metabarcoding methodology. On the other hand, no specifically methanogenic group was detected in significant abundance. To future application using culturomics approaches to bioremediation the leachate sample presented groups extensively studied, especially the Pseudomonas genus to heavy metals treatments, such as cadmium.

Levels of Firmicutes, Actinobacteria Phyla and Lactobacillaceae Family on the Skin Surface of Broiler Chickens (Ross 308) Depending on the Nutritional Supplement and the Housing Conditions

The microbiome of animals, both in the digestive tract and in the skin, plays an important role in protecting the host. The skin is one of the largest surface organs for animals; therefore, the destabilization of the microbiota on its surface can increase the risk of diseases that may adversely affect animals’ health and production rates, including poultry. The aim of this study was to evaluate the effect of nutritional supplementation in the form of fermented rapeseed meal and housing conditions on the level of selected bacteria phyla (Firmicutes, Actinobacteria, and family Lactobacillaceae). The study was performed on 30 specimens of broiler chickens (Ross 308), individually kept in metabolic cages for 36 days. They were divided into 5 groups depending on the feed received. On day 36, skin swabs were individually collected. Temperature and humidity were measured in the room. The temperature was measured every 2 days (18 measurements × 6 points). The results of Real-Time PCR analysis have shown a significant effect of the feed additive on the level of Firmicutes phylum on the skin. On the other hand, a variable level of the tested bacteria was shown depending on the location of the cages. The Firmicutes phylum and Lactobacillaceae family achieved the highest level in the top-window zone. However, in the case of the Actinobacteria phylum, the highest level was found at the top-door and middle-door zones. The obtained results suggest that the conditions in which animals live may affect the microbiota of their skin.

Lifestyle modifications result in alterations in the gut microbiota in obese children

Background The association between the gut microbiota and pediatric obesity was analyzed in a cross-sectional study. A prospective study of obese children was conducted to assess the gut microbial alterations after a weight change. We collected fecal samples from obese children before and after a 2-month weight reduction program that consisted of individual counseling for nutritional education and physical activity, and we performed 16S rRNA gene amplicon sequencing using an Illumina MiSeq platform. Results Thirty-six participants, aged 7 to 18 years, were classified into the fat loss (n = 17) and the fat gain (n = 19) groups according to the change in total body fat (%) after the intervention. The baseline analysis of the gut microbiota in the preintervention stages showed dysbiotic features of both groups compared with those of normal-weight children. In the fat loss group, significantly decreased proportions of Bacteroidetes phylum, Bacteroidia class, Bacteroidales order, Bacteroidaceae family, and Bacteroides genus, along with increased proportions of Firmicutes phylum, Clostridia class, and Clostridiales order, were observed after intervention. The microbial richness was significantly reduced, without a change in beta diversity in the fat loss group. The fat gain group showed significantly deceased proportions of Firmicutes phylum, Clostridia class, Clostridiales order, Lachnospiraceae family, and Eubacterium hallii group genus, without a change in diversity after the intervention. According to the functional metabolic analysis by the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2, the “Nitrate Reduction VI” and “Aspartate Superpathway” pathways were predicted to increase significantly in the fat loss group. The cooccurring networks of genera were constructed and showed the different microbes that drove the changes between the pre- and postintervention stages in the fat loss and fat gain groups. Conclusions This study demonstrated that lifestyle modifications can impact the composition, richness, and predicted functional profiles of the gut microbiota in obese children after weight changes. Trial registration ClinicalTrials.govNCT03812497, registration date January 23, 2019, retrospectively registered.

NEAr Transporter (NEAT) Domains: Unique Surface Displayed Heme Chaperones That Enable Gram-Positive Bacteria to Capture Heme-Iron From Hemoglobin

Iron is an important micronutrient that is required by bacteria to proliferate and to cause disease. Many bacterial pathogens forage iron from human hemoglobin (Hb) during infections, which contains this metal within heme (iron–protoporphyrin IX). Several clinically important pathogenic species within the Firmicutes phylum scavenge heme using surface-displayed or secreted NEAr Transporter (NEAT) domains. In this review, we discuss how these versatile proteins function in the Staphylococcus aureus Iron-regulated surface determinant system that scavenges heme-iron from Hb. S. aureus NEAT domains function as either Hb receptors or as heme-binding chaperones. In vitro studies have shown that heme-binding NEAT domains can rapidly exchange heme amongst one another via transiently forming transfer complexes, leading to the interesting hypothesis that they may form a protein-wire within the peptidoglycan layer through which heme flows from the microbial surface to the membrane. In Hb receptors, recent studies have revealed how dedicated heme- and Hb-binding NEAT domains function synergistically to extract Hb’s heme molecules, and how receptor binding to the Hb-haptoglobin complex may block its clearance by macrophages, prolonging microbial access to Hb’s iron. The functions of NEAT domains in other Gram-positive bacteria are also reviewed.

Correlation Between Gut Microbiome Composition and Acute Pain Perception in Young Healthy Male Subjects

Objective Recently, there has been growing interest in the gut–brain axis because it is emerging as a player influencing the health status of the host human. It is a known fact that the gut microbiome (GM) through the gut–brain axis has been implicated in numerous diseases. We previously reported that stool condition was associated with pain perception. Stool consistency and constipation are known to be associated with GM composition. Thus, we imagine that GM composition could influence pain perception. The aim of this study was to investigate the correlations between GM composition and pain perception and psychological states in young healthy male subjects. Subjects A total of 42 healthy young male volunteers completed the present study. Methods The volunteers’ pain perceptions were assessed by pressure pain threshold, current perception threshold, temporal summation of pain, and conditioned pain modulation, and a questionnaire on psychological state was obtained. During the current perception threshold examination, we used 5, 250, and 2,000 Hz to stimulate C, Aδ, and Aβ fibers. In addition, GM composition was evaluated by using 16S rRNA analysis. Results Pressure pain threshold showed a significant and negative correlation with Bacteroidetes phylum, in contrast to a significant and positive correlation with Firmicutes phylum. Current perception threshold of Aδ and Firmicutes phylum showed a significant correlation. There was a negative correlation between anxiety state and Bifidobacterium genus. In contrast, there was no significant correlation between psychological states and pain perceptions. Conclusion The present study showed that acute pain perception was associated with GM composition in young healthy males.

PSVIII-21 The effect of medicinal extracts on microflora and enzymatic processes of calf rumen

The fight against antibiotic resistance and a decrease in the greenhouse effect leads to the search for safe alternative substances for animals, special attention is paid to phytochemicals in medicinal plants. The aim of this study was to evaluate the effect of extracts of Oríganum vulgáre (OV) and Hypéricum perforátum (HP; 0.5 ml/kg body weight) on ruminal microflora and fermentation characteristics against the background of control (C). The extracts were added to water of bulls with rumen fistula (14-month, diet - 70% hay, 30% barley grain). The fermentation parameters (CH4, digestibility of dry matter of the grain) were analyzed daily, and the microflora was analyzed using highly efficient sequencing of 16S rRNA gene (Illumina). OV and HP were prepared by grinding, extraction in a water bath (30 min, 70 ° C) and filtration. According to the results, the addition of OV and HP reduces the formation of CH4 and the digestibility of CB did not differ compared to C (48.7 and 47.8%, against 50.6%). The phylum of archaea Euryarchaeota was small and dominant in OV and HP. The phylum of Bacteroidetes dominated and was higher than that of C, that of OV was 35.6% (P ≤ 0.05) and HP was 30.7% (P ≤ 0.05). The Bacteroidia class (30.0–31.5%) changed similarly due to the families Porphyromonadaceae (P ≤ 0.05), Prevotellaceae (P ≤ 0.05). OV showed a tendency towards a decrease in Firmicutes phylum, and increase in bacteria of the Clostridia class by 11.1% (P ≤ 0.05). Clostridia class prevailed in HP by 14.5% (P ≤ 0.05) in comparison with C, due to Ruminococcaceae, Clostridiales families. This study highlights the potential use of OV and HP in cattle diets aimed at decreasing methane production and increasing gram-negative bacteria. This research was performed with financial support from the RSF (16-16-10048) and project 0761-2019-0005.

Oatmeal induced gut microbiota alteration and its relationship with improved lipid profiles: a secondary analysis of a randomized clinical trial

Background In vitro and animal experiments reported a microbiota-regulating ability of oatmeal, however, related in vivo evidences remained limited. Thus, we conducted this study aiming to investigate the oatmeal-induced alteration of gut microbiota and its potential relationship with the improvements of lipid profiles. Methods and study design Data of anthropometric measurements and biochemical parameters were extracted from a randomized, controlled clinical trial, in which 62 hypercholesterolemic men and women (18–65 years old) were provided with either treatment of 80 g/day oatmeal or 80 g/day refined white rice for 45 days. Fasting blood samples and fecal samples were collected both at baseline and endpoint of the study for lipid profiling and microbiota 16S rRNA amplicon sequencing, respectively. Results Totally 28 participants (56 fecal samples) qualified with the new criteria and were thus included in this secondary analysis. The results of microbiota analysis showed that no significant difference was observed in the alteration of its overall α or β diversity between two groups throughout the study. Nor did any notable between-group difference was found in the relative abundance changes of microorganism at different taxonomies. However, results from linear discriminant analysis effect size in the oatmeal group indicated a significant positive response of Firmicutes phylum following oatmeal consumption. Further Procrustes analysis suggested a concordance trend between microorganism alteration and alleviation of hypercholesterolemia phenotypes throughout the study (P = 0.05). The results of within-group comparison from Spearman’s correlation in the oatmeal group demonstrated a significant association between the enrichment of Blautia genus and the reduction of serum total cholesterol (P < 0.05), low-density lipoprotein cholesterol (P < 0.01), and apolipoprotein B (P < 0.05). Conclusions Positive response of Firmicutes phylum might be a critical characteristic of oatmeal-induced alteration of microbiota, whereas, one of the underlying cholesterol-lowering mechanism of oatmeal consumption might be its microbiota-manipulating ability, in which the enrichment of Blautia genus played a potentially significant role. Current results should be taken cautiously and more studies were needed for further verification. Trial registration: ChiCTR, ChiCTR180001864. Registered 30 September 2018, http://www.chictr.org.cn/showproj.aspx?proj=31469.

The intestinal microbiota in psoriasis

Microbiota is a kind of ecosystem inhabiting some organs, supporting their proper functioning, but also having a significant impact on the development of the immune system. The largest reservoir of microbiota is the digestive tract, where the largest number of lymphocytes is also present. Literature gradually increases the number of studies assessing the relationship between intestinal dysbiosis and the development of various parenteral diseases. This article presents the latest data from the medical literature regarding intestinal microbiota and barrier in patients with psoriasis. In the cited studies, a quantitative advantage of Firmicutes phylum over Bacteroidetes phylum and a smaller colonization of Actinobacteria phylum has been demonstrated. In terms of the species, colonization of bacteria Faecalibacterium prausnitzii and Akkermansia muciniphilia was reduced, and Escherichia coli increased. Regarding the participation of individual taxonomic units, the results in the cited studies are partly different. However, all revealed significant differences between the intestinal microbiota of patients with psoriasis and a healthy population, which suggests the importance of intestinal dysbiosis in the development of this disease. It seems more important that what leads to disturbances in the metabolic balance is not so much the quantity of individual taxonomic units as their disproportions. In some studies, the deviations in microbiota correlated with the level of metabolites and indicators of inflammation. Moreover, some studies revealed a significantly higher incidence of Candida in the oral cavity as well as in the stool samples of patients with psoriasis. There are also reports in the literature in which the occurrence of intestinal inflammation and the impairment of the intestinal barrier in patients with psoriasis have been demonstrated. These observations indicate interrelations between psoriasis and intestinal disorders as well as the involvement of dysbiosis in both associations and the pathogenesis of psoriasis.