Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation.

Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia (Borkfalkiaceae, Lachnospiraceae, Monoglobaceae, and Oscillospiraceae families) and Bacilli (Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia, Bacilli, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia, Bacilli, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.

Isolation and Characterization of Thermophilic Bacteria from a Hot Spring in the State of Hidalgo, Mexico, and Geochemical Analysis of the Thermal Water.

Hot springs worldwide can be a source of extremophilic microorganisms of biotechnological interest. In this study, samplings of a hot spring in Hidalgo, Mexico, were conducted to isolate, identify, and characterize morphologically, biochemically, and molecularly those bacterial strains with potential industrial applications. In addition, a physicochemical and geochemical examination of the hot spring was conducted to fully understand the study region and its potential connection to the strains discovered. The hot spring was classified as sulfate-calcic according to the Piper Diagram; the hydrogeochemical analysis showed the possible interactions between minerals and water. Eighteen bacterial strains were isolated with optimal growth temperatures from 50 to 55 °C. All strains are Gram-positive, the majority having a rod shape, and one a round shape, and 17 produce endospores. Hydrolysis tests on cellulose, pectin, and xylan agar plates demonstrated enzymatic activity in some of the strains. Molecular identification through the 16S rDNA gene allowed classification of 17 strains within the Phylum Firmicutes and one within Deinococcus-Thermus. The bacterial strains were associated with the genera Anoxybacillus, Bacillus, Anerunibacillus, Paenibacillus, and Deinococcus, indicating a diversity of bacterial strains with potential industrial applications.

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.

Accelerometer-based sleep metrics and gut microbiota during adolescence: Association findings from a Brazilian population-based birth cohort.

BACKGROUND: Sleep and gut microbiota are emerging putative risk factors for several physical, mental, and cognitive conditions. Sleep deprivation has been shown to be linked with unhealthy microbiome environments in animal studies. However, in humans, the results are mixed. Epidemiological studies evaluating the effect of accelerometer-based sleep measures on gut microbiome are scarce. This study aims to explore the relationship between sleep duration and efficiency with the gut microbiota in adolescence. METHODS: A subsample of 352 participants from the 2004 Pelotas (Brazil) Birth Cohort Study with sleep and fecal microbiota data available were included in the study. Sleep duration and sleep efficiency were obtained from actigraphy information at 11 years old whereas microbiota information from fecal samples was collected at 12 years. The fecal microbiota was analyzed via Illumina MiSeq (16S rRNA V3-V4 region) and the UNOISE pipeline. Alpha was assessed in QIIME2. Association measures for sleep variables and microbial α-diversity, and bacterial relative abundance were assessed through generalized models (linear and logistic regression), adjusting for maternal and child variables confounders. RESULTS: Adjusted models showed that sleep duration was positively associated with Simpson index of α-diversity (ß = 0.003; CI95 %: 0.00004; 0.01). Both sleep duration (OR = 0.43; CI95 % 0.25; 0.74) and efficiency (OR = 0.55; CI95 % 0.38; 0.78) were associated with lower Bacteroidetes abundance. CONCLUSION: Our results suggest that sleep duration and efficiency are linked to gut microbiota diversity and composition even with 1-2 years gap from exposure to outcome. The findings support the role of sleep in the gut-brain axis as well as provide insights on how to improve microbiota health.

Effect of whole oilseeds in the diet on bacterial diversity in the solid fraction of the ruminal content of steers.

Our hypothesis was that different whole oilseeds included in the diet for steers confined could alter the diversity of rumen bacteria compared to a diet without oilseeds or an exclusively forage diet. It was aimed to evaluate the effects of oilseeds inclusion in the diet on bacterial diversity in the solid fraction of the ruminal content of steers, by gene sequences of the conserved 16S rDNA region. Six crossbred steers castrated males, fitted with ruminal cannula were used in a 6 × 6 Latin square design, using 21-day period. At the start of the experiment, the live weight of the animals averaged 416 ± 9.7 kg (mean ± SD). A total of 2,180,562 16S rDNA sequences were generated for the Bacteria domain by MiSeq sequencing. The bacterial diversity was composed of 24 bacterial phyla, with the most abundant being Firmicutes, Bacteroidetes, and Proteobacteria. Other phyla with less diversity were also identified including Eurychaeota, Tenericutes, SR1 Absconditalbacteria, Synergistetes, Actinobacteria, Saccharibacteria, Elusimicrobia, Cyanobacteria, Verrucomicrobia, Fusobacteria, Lentisphaerae. The similarity in the bacterial community averaged 50% for all the experimental diets. Steers-fed corn silage exhibited a great diversity of bacteria of the Firmicutes phylum. The steers-fed oilseeds in the diet had a great diversity of bacteria from the phylum Bacteroidetes and Proteobacteria. The inclusion of whole oilseeds in the steer diets can alter the rumen bacteria population by up to 50% of total diversity.

Alteración de la microbiota intestinal y su relación con enfermedades gastrointestinales y hepatobiliares / Disruption of the intestinal microbiota and its relationship with gastrointestinal and hepatobiliary diseases

La interrupción de la simbiosis que existe entre el cuerpo humano y su microbioma puede resultar en una disbiosis, un desequilibrio en la interacción huésped-microbiota, que puede asociarse al desarrollo de diversas enfermedades como el síndrome de intestino irritable, hígado graso no alco-hólico, enfermedad hepática alcohólica y cirrosis, entre otras. En ciertas condiciones patológicas y por múltiples factores de riesgo, la capacidad de autorregulación del intestino se puede alterar, contribuyendo al incremento de la permeabilidad con inflamación intestinal crónica. El diagnóstico y el tratamiento, así como la relación entre la permeabilidad intestinal, la disbiosis y las patologías gastrointestinales y hepatobiliares, todavía no tienen estudios clínicos validados o con el soporte científico adecuado, por lo que se realiza una revisión de la literatura con la finalidad de aportar conceptos que puedan orientar con respecto a la importancia del estudio del microbioma humano en estas enfermedades.

Disruption of the symbiosis that exists between the human body and its microbiome can result in dys-biosis, an imbalance in the host-microbiota interaction, which may be associated with the develop-ment of various diseases such as irritable bowel syndrome, non-alcoholic fatty liver disease, alcoholic liver disease and cirrhosis, among others. In certain pathological conditions and due to multiple risk factors, the self-regulating capacity of the intestine may be lost, contributing to increased permeability with chronic intestinal inflammation. Its diagnosis and treatment as well as the relationship between intestinal permeability, dysbiosis and gastrointestinal and hepatobiliary pathologies have not been validated in clinical studies or have adequate scientific support, so a review of the literature is carried out in order to provide concepts that can guide with respect to the importance of the study of the human microbiome in these diseases

Chronic-Antibiotics Induced Gut Microbiota Dysbiosis Rescues Memory Impairment and Reduces ß-Amyloid Aggregation in a Preclinical Alzheimer's Disease Model.

Alzheimer's disease (AD) is a multifactorial pathology characterized by ß-amyloid (Aß) deposits, Tau hyperphosphorylation, neuroinflammatory response, and cognitive deficit. Changes in the bacterial gut microbiota (BGM) have been reported as a possible etiological factor of AD. We assessed in offspring (F1) 3xTg, the effect of BGM dysbiosisdysbiosis in mothers (F0) at gestation and F1 from lactation up to the age of 5 months on Aß and Tau levels in the hippocampus, as well as on spatial memory at the early symptomatic stage of AD. We found that BGM dysbiosisdysbiosis with antibiotics (Abx) treatment in F0 was vertically transferred to their F1 3xTg mice, as observed on postnatal day (PD) 30 and 150. On PD150, we observed a delay in spatial memory impairment and Aß deposits, but not in Tau and pTau protein in the hippocampus at the early symptomatic stage of AD. These effects are correlated with relative abundance of bacteria and alpha diversity, and are specific to bacterial consortia. Our results suggest that this specific BGM could reduce neuroinflammatory responses related to cerebral amyloidosis and cognitive deficit and activate metabolic pathways associated with the biosynthesis of triggering or protective molecules for AD.

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.

Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone.

BACKGROUND: Pseudalcantarea grandis (Schltdl.) Pinzón & Barfuss is a tank bromeliad that grows on cliffs in the southernmost portion of the Chihuahuan desert. Phytotelmata are water bodies formed by plants that function as micro-ecosystems where bacteria, algae, protists, insects, fungi, and some vertebrates can develop. We hypothesized that the bacterial diversity contained in the phytotelma formed in a bromeliad from an arid zone would differ in sites with and without surrounding vegetation. Our study aimed to characterize the bacterial composition and putative metabolic functions in P. grandis phytotelmata collected in vegetated and non-vegetated sites. METHODS: Water from 10 individuals was sampled. Five individuals had abundant surrounding vegetation, and five had little or no vegetation. We extracted DNA and amplified seven hypervariable regions of the 16S gene (V2, V4, V8, V3-6, 7-9). Metabarcoding sequencing was performed on the Ion Torrent PGM platform. Taxonomic identity was assigned by the binning reads and coverage between hit and query from the reference database of at least 90%. Putative metabolic functions of the bacterial families were assigned mainly using the FAPROTAX database. The dominance patterns in each site were visualized with rank/abundance curves using the number of Operational Taxonomic Units (OTUs) per family. A percentage similarity analysis (SIMPER) was used to estimate dissimilarity between the sites. Relationships among bacterial families (identified by the dominance analysis and SIMPER), sites, and their respective putative functions were analyzed with shade plots. RESULTS: A total of 1.5 million useful bacterial sequences were obtained. Sequences were clustered into OTUs, and taxonomic assignment was conducted using BLAST in the Greengenes databases. Bacterial diversity was 23 phyla, 52 classes, 98 orders, 218 families, and 297 genera. Proteobacteria (37%), Actinobacteria (19%), and Firmicutes (15%) comprised the highest percentage (71%). There was a 68.3% similarity between the two sites at family level, with 149 families shared. Aerobic chemoheterotrophy and fermentation were the main metabolic functions in both sites, followed by ureolysis, nitrate reduction, aromatic compound degradation, and nitrogen fixation. The dominant bacteria shared most of the metabolic functions between sites. Some functions were recorded for one site only and were related to families with the lowest OTUs richness. Bacterial diversity in the P. grandis tanks included dominant phyla and families present at low percentage that could be considered part of a rare biosphere. A rare biosphere can form genetic reservoirs, the local abundance of which depends on external abiotic and biotic factors, while their interactions could favor micro-ecosystem resilience and resistance.

Ten-Week Sucralose Consumption Induces Gut Dysbiosis and Altered Glucose and Insulin Levels in Healthy Young Adults.

Sucralose consumption alters microbiome and carbohydrate metabolism in mouse models. However, there are no conclusive studies in humans. Our goals were to examine the effect of sucralose consumption on the intestinal abundance of bacterial species belonging to Actinobacteria, Bacteroidetes, and Firmicutes and explore potential associations between microbiome profiles and glucose and insulin blood levels in healthy young adults. In this open-label clinical trial, volunteers randomly drank water, as a control (n = 20), or 48 mg sucralose (n = 20), every day for ten weeks. At the beginning and the end of the study, participants were subjected to an oral glucose tolerance test (OGTT) to measure serum glucose and insulin every 15 min for 3 h and provided fecal samples to assess gut microbiota using a quantitative polymerase chain reaction. Sucralose intake altered the abundance of Firmicutes without affecting Actinobacteria or Bacteroidetes. Two-way ANOVA revealed that volunteers drinking sucralose for ten weeks showed a 3-fold increase in Blautia coccoides and a 0.66-fold decrease in Lactobacillus acidophilus compared to the controls. Sucralose consumption increased serum insulin and the area under the glucose curve compared to water. Long-term sucralose ingestion induces gut dysbiosis associated with altered insulin and glucose levels during an OGTT.

Characterization of the Cafeteria Diet as Simulation of the Human Western Diet and Its Impact on the Lipidomic Profile and Gut Microbiota in Obese Rats.

The obesity pandemic has been strongly associated with the Western diet, characterized by the consumption of ultra-processed foods. The Western lifestyle causes gut dysbiosis leading to impaired fatty acid metabolism. Therefore, this study aimed to evaluate shifts in gut microbiota and correlate these with serum fatty acid profiles in male Wistar rats fed a cafeteria diet. Ten male rats were fed with standard diet (CTL, n = 5) and cafeteria diet (CAF, n = 5) for fifteen weeks. Body weight and food intake were recorded once and three times per week, respectively. At the end of the study, fresh fecal samples were collected, tissues were removed, and serum samples were obtained for further analyses. Gut microbiota was analyzed by sequencing the V3-V4 region of 16S rRNA gene. Serum fatty acid profiles were fractioned and quantified via gas chromatography. The CAF diet induced an obese phenotype accompanied by impaired serum fatty acids, finding significantly higher proportions of total saturated fatty acids (SFAs) and C20:3 n-6, and lower C18:1 n-7 and C18:3 n-3 in the phospholipid (PL) fraction. Furthermore, circulating C10:0, total n-3 and n-7 decreased and total monounsaturated fatty acids (MUFAs), including oleic acid C18:1 n-9, increased in the cholesterol ester (CE) fraction. The obesity metabotype may be mediated by gut dysbiosis caused by a cafeteria diet rich in C16:0, C18:0, C18:1 n-9 and C18:2 n-6 fatty acids resulting in a 34:1 omega-6/omega-3 ratio. Therefore, circulating C10:0 was associated with several genera bacteria such as Prevotella (positive) and Anaerotruncus (negative). Two classes of Firmicutes, Bacilli and Erysipelotrichi, were positively correlated with PL- C20:3 n-6 and CE- 18:1 n-9, respectively. TM7 and Bacteroidetes were inversely correlated with PL-SFAs and CE- 18:2 n-6, respectively.

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.

Characteristics of faecal bacterial flora and volatile fatty acids in Min pig, Landrace pig, and Yorkshire pig

BACKGROUND In order to study the influence of long-term growth process and evolution environment on intestinal bacteria of different breeds, the intestinal bacteria and volatile fatty acids among the faeces of Min, Landrace and Yorkshire pigs were analysed by Illumina high-throughput sequencing of the 16S-rDNA and gas chromatography. RESULTS The shared core microbiota of Landrace, Yorkshire and Min pig were 1273, accounting for 69.56% of total abundance of organisms. The proportion of Firmicutes in Min pig faeces (57.89%) was significantly higher than that in Landrace and Yorkshire pig faeces (47.01% and 46.40%, respectively) (P < 0.05), but that of Bacteroidetes was exactly opposite. Moreover, Min pig presented more highly efficient membrane transport, environmental adaptation, carbohydrate transport, and metabolism than Yorkshire pig (P < 0.05). The acetic acid/total volatile fatty acid ratio in Min pig was significantly higher than that in Landrace pig (P < 0.05), and the isobutyric acid/ total volatile fatty acid ratio in Min pig was significantly larger than that in Yorkshire pig (P < 0.05). Furthermore, the content of branched chain volatile fatty acids in Min pig was significantly higher than that in Yorkshire pig (P < 0.05). CONCLUSION This study demonstrated that Min pig, as an excellent breed in the cold area of China, possessed special intestinal floral structure compared to the imported pigs in order to satisfy their phys iological and metabolic demands, which may influence their characteristics such as resistance to cold, diseases, and crude feeding, and the ability to deposit intramuscular fat.

Altered milk yield and rumen microbial abundance in response to concentrate supplementation during the cold season in Tibetan sheep

BACKGROUND Weight loss and decline of milk yield in Tibetan sheep was a challenge for the dairy industry in Qinghai-Tibet Plateau, which were considered to be caused by underfeeding of the sheep during the harsh winter. The objective of this study was to assess the role of feed supplementation in the milk performance and rumen microbiome of ewes under forage-based diets. Based on parity, milking period, milk yield, and body weight, ten 1.5-yr-old ewes were allocated randomly into two groups. One group of ewes was fed no supplement Control group (CON) and the other group was fed with concentrate feed supplement (Treatment group, T). Individual milk yield was determined daily; both the milk composition and rumen bacterial characteristics were analyzed after the end of feeding trials. RESULTS Results showed that lactose in the milk of the CON group was significantly lower (P < 0.05) than that of the T group at days 30 and 60. Milk yield in the T group was greater than in the CON group at day 30 (P < 0.05). Additionally, the dominant ruminal bacteria (phyla Bacteroidetes, Firmicutes, and Verrucomicrobia) were shared by both groups through 16S rRNA gene pyrosequencing. Greater relative abundance of Bacteroidales RF16 group in family level, Victivallales in order level, Lentisphaeria in class level, and Lachnospiraceae bacterium in species level were observed in the T group than in the CON group (P < 0.05). CONCLUSIONS These results demonstrated that supplementation of concentrate in the cold season improved milk lactose yield and milk production, and the rumen microbial abundance of Tibetan sheep.

Firmicutes Levels in the Mouth Reflect the Gut Condition With Respect to Obesity and Early Childhood Caries.

The present cross-sectional study investigated whether Firmicutes (F) and Bacteroidetes (B) levels in the mouth reflected the gut condition in obesity and early childhood caries (ECC). Eighty preschoolers (3-5 years) were equally assigned into four groups: 1. obese + ECC, 2. obese + caries-free (CF), 3. eutrophic + ECC, and 4. eutrophic + CF. Nutritional status and ECC were assessed based on the WHO criteria. Dental biofilm and fecal samples were collected for F and B quantification using RT-PCR analysis. Data were evaluated using three-way-ANOVA and Pearson's correlation (α = 0.05). Regardless of the anatomical location effect (p = 0.22), there were higher values for F in the obese children + ECC compared with those in obese + caries-free (CF) in both mouth and gut (p < 0.05). The correlation for F at these sites was negative in obese children + ECC (r = -0.48; p = 0.03) and positive in obese children + CF (r=0.50; p = 0.03). Bacteroidetes were influenced by ECC (p = 0.03) and the anatomical location (p = 0.00), and the levels tended to be higher in the mouth of the obese children + ECC (p = 0.04). The F/B ratio was higher in the gut and was affected by the anatomical location (p = 0.00). This preliminary study suggested that modulated by ECC, counts of oral Firmicutes reflected corresponding condition in the gut of obese preschoolers. In addition, we first evidenced that the Firmicutes phylum behave differently according to the nutritional status and caries experience and that supragingival biofilm and gut could share levels of similarity.

Green banana flour supplementation improves obesity-associated systemic inflammation and regulates gut microbiota profile in mice fed high-fat diets.

This study evaluated the effect of green banana flour (GBF) consumption on obesity-related conditions in mice fed high-fat diets. GBF was prepared using stage 1 green banana pulp, which was dehydrated and milled. Mice were fed a control diet (n = 20; 10% of energy from lipids) or a high-fat diet (n = 20; 50% of energy from lipids). After 10 weeks, mice were divided into 4 groups based on feed: standard chow (SC; n = 10), standard with 15% GBF (SB; n = 10), high-fat diet (HF; n = 10) and high-fat diet with 15% GBF (HFB; n = 10) for 4 weeks. HFB exhibited lower gains in body weight (-21%; p < 0.01) and in all fat pads (p < 0.01) compared with the HF group. SC, SB, and HFB showed smaller retroperitoneal white adipose tissue diameters (p < 0.001). SB and HFB-treated mice showed lower levels of leptin, IL-6, and TNF-α compared with the SC and HF groups (p < 0.01). In the GBF-fed groups, there was a reduction in the abundance of Firmicutes (SB: -22%; HFB: -23%) and an increase in Bacteroidetes (SB: +25%; HFB: +29%) compared with their counterparts. We demonstrated that GBF consumption attenuated inflammation and improved metabolic status, adipose tissue remodeling, and the gut microbiota profile of obese mice. Novelty: Green banana flour (GBF) consumption, rich in resistant starch, regulates body weight in mice fed high-fat diets. GBF consumption improves fat pad distribution in mice fed high-fat diets. GBF improves obesity-associated systemic inflammation and regulates gut microbiota profile in mice fed high-fat diets.

Metagenomics approach to identify lignocellulose-degrading enzymes in the gut microbiota of the Chinese bamboo rat cecum

BACKGROUND: Lignocellulose is considered a renewable organic material, but the industrial production of biofuel from lignocellulose is challenging because of the lack of highly active hydrolytic enzymes. The guts of herbivores contain many symbiotic microorganisms that have evolved to hydrolyze plant lignocellulose. Chinese bamboo rats mainly consume high-fiber foods, indicating that some members of the intestinal tract microbiota digest lignocellulose, providing these rats with the energy required for growth. RESULTS: Here, we used metagenomics to analyze the diversity and functions of the gut microbiota in Chinese bamboo rats. We identified abundant populations of lignocellulose-degrading bacteria, whose main functions involved carbohydrate, amino acid, and nucleic acid metabolism. We also found 587 carbohydrate-active enzyme genes belonging to different families, including 7 carbohydrate esterase families and 21 glycoside hydrolase families. The glycoside hydrolase 3, glycoside hydrolase 1, glycoside hydrolase 43, carbohydrate esterase 4, carbohydrate esterase 1, and carbohydrate esterase 3 families demonstrated outstanding performance. CONCLUSIONS: The microbes and enzymes identified in our study expand the existing arsenal of proficient degraders and enzymes for lignocellulosic biofuel production. This study also describes a powerful approach for targeting gut microbes and enzymes in numerous industries.

Changes in freshwater sediment microbial populations during fermentation of crude glycerol

BACKGROUND: This work studied how the exposure to an unusual substrate forced a change in microbial populations during anaerobic fermentation of crude glycerol, a by-product of biodiesel production, with freshwater sediment used as an inoculum. RESULTS: The microbial associations almost completely (99.9%) utilized the glycerol contained in crude glycerol 6 g L 1 within four days, releasing gases, organic acids (acetic, butyric) and alcohols (ethanol, n-butanol) under anaerobic conditions. In comparison with control medium without glycerol, adding crude glycerol to the medium increased the amount of ethanol and n-butanol production and it was not significantly affected by incubation temperature (28 C or 37 C), nor incubation time (4 or 8 d), but it resulted in reduced amount of butyric acid. Higher volume of gas was produced at 37 C despite the fact that the overall bacterial count was smaller than the one measured at 20 C. Main microbial phyla of the inoculum were Actinobacteria, Proteobacteria and Firmicutes. During fermentation, significant changes were observed and Firmicutes, especially Clostridium spp., began to dominate, and the number of Actinobacteria and Gammaproteobacteria decreased accordingly. Concentration of Archaea decreased, especially in medium with crude glycerol. These changes were confirmed both by culturing and culture-independent (concentration of 16S rDNA) methods. CONCLUSIONS: Crude glycerol led to the adaptation of freshwater sediment microbial populations to this substrate. Changes of microbial community were a result of a community adaptation to a new source of carbon.

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients?

The gut microbiota is emerging as a promising target for the management or prevention of inflammatory and metabolic disorders in humans. Many of the current research efforts are focused on the identification of specific microbial signatures, more particularly for those associated with obesity, type 2 diabetes, and cardiovascular diseases. Some studies have described that the gut microbiota of obese animals and humans exhibits a higher Firmicutes/Bacteroidetes ratio compared with normal-weight individuals, proposing this ratio as an eventual biomarker. Accordingly, the Firmicutes/Bacteroidetes ratio is frequently cited in the scientific literature as a hallmark of obesity. The aim of the present review was to discuss the validity of this potential marker, based on the great amount of contradictory results reported in the literature. Such discrepancies might be explained by the existence of interpretative bias generated by methodological differences in sample processing and DNA sequence analysis, or by the generally poor characterization of the recruited subjects and, more particularly, the lack of consideration of lifestyle-associated factors known to affect microbiota composition and/or diversity. For these reasons, it is currently difficult to associate the Firmicutes/Bacteroidetes ratio with a determined health status and more specifically to consider it as a hallmark of obesity.

Composition of the bacterial community in the gastrointestinal tract of Kunming mice

Background: The intestinal bacterial community has an important role in maintaining human health. Dysbiosis is a key inducer of many chronic diseases including obesity and diabetes. Kunming mice are frequently used as a model of human disease and yet little is known about the bacterial microbiome resident to the gastrointestinal tract. Results: We undertook metagenomic sequencing of the luminal contents of the stomach, duodenum, jejunum, ileum, cecum, colon, and rectum of Kunming mice. Firmicutes was the dominant bacterial phylum of each intestinal tract and Lactobacillus the dominant genus. However, the bacterial composition differed among the seven intestinal tracts of Kunming mice. Compared with the small intestine, the large intestine bacterial community of Kunming mice is more stable and diverse. Conclusions: To our knowledge, ours is the first study to systematically describe the gastrointestinal bacterial composition of Kunming mice. Our findings provide a better understanding of the bacterial composition of Kunming mice and serves as a foundation for the study of precision medicine.