Search Results (7,047)

Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as Polaromonas, Macrococcus, and Agitococcus, resulting in increased relative abundance (p < 0.5) up to 5.0 log fold change compared to VF, rendering SMF inapplicable for bacterial microbiome studies. The best-performing DNA extraction protocols were FastSpin Soil, the in-house method, and EurX. All 16S-DBs yielded comparable MIQ scores within each DNA extraction kit, ranging from 61–66 (ZymoBIOMICs) up to 80–82 (FastSpin). DNA extraction kits exert more bias toward the composition than 16S-DBs. This benchmarking study provided valuable information to inform future water metagenomic study designs. Full article

Inonotus hispidus (Bull.) P. Karst., is a medicinal fungus, which parasitizes broad-leaved tree such as Morus alba L., Fraxinus mandshurica Rupr., and Ulmus macrocarpa Hance. To elucidate the internal relationship between I. hispidus and its hosts, this study analyzed endophytic bacteria and fungi in the roots of M. alba and F. mandshurica growing I. hispidus using the 16S rDNA and ITS high-throughput sequencing technologies; and conducted widely targeted metabolomics research using UPLC-MS/MS. The results showed that Cyanobacteria and unidentified chloroplasts had the highest relative abundance at the phylum and genus levels, respectively. For endophytic fungi, Ascomycota was dominant at the phylum level, while Pleosporales gen Incertae sedis and Oncopodiella were the dominant genera in the roots of M. alba and F. mandshurica, respectively. Widely targeted metabolomics identified 562 differential metabolites and 46 metabolic pathways. Correlation analysis revealed that Xanthobacteraceae, Pseudorhodoplanes, and Bauldia were potential regulators of phenolic acids and phenylpropanoids biosynthesis. Additionally, the genus Oncopodiella was primarily associated with the enrichment of lipids, amino acids, sugars, phenolic acids, and other compounds. This result provides significant insights into the size of the fruiting body, resource development, and active ingredients of I. hispidus from different tree sources. Full article

Background: Vaginal Lactobacillus predominance is associated with improved vaginal health and reduced pregnancy complications. Little is known about how dietary quality may improve vaginal microbial composition or about dietary interventions that may promote Lactobacillus abundance. To understand the host factors affecting vaginal microbiota during pregnancy in a multi-ethnic cohort in Hawai`i. We hypothesize that better diet quality improves vaginal microbial composition, as represented by Lactobacillus abundance and depletion of anaerobic organisms. Methods: We compared comprehensive diet quality, as measured by the Healthy Eating Index-2015 (HEI-2015), to taxonomic classifications of bacteria present within the vagina. Participants of the four predominant ethnic groups in Hawai’i (Japanese, Filipino, Non-Hispanic White and Native Hawaiian) completed Quantitative Food Frequency Questionnaires (QFFQs) and collected vaginal swabs during each trimester. 16s rRNA amplicon sequencing (V2–V9 regions) was performed on vaginal samples. HEI-2015 scores and macro- and micronutrient intake were compared with the predominant species present using the Mann–Whitney-U test, PERMANOVA, and the Pearson correlation coefficient. A mixed-effects logistics regression model was used to predict the depletion of Lactobacillus species while accounting for confounding demographic factors. Results: Matched, longitudinal data for 40 participants demonstrated three predominant Lactobacillus species: L. crispatus, L. iners, and L. gasseri, with another subset of samples with anaerobic abundance. (Primarily, Atopobium vaginae, Prevotella, and Gardnerella vaginalis.) Non-Hispanic White participants had lower amounts of Lactobacillus iners compared to other racial and ethnic groups. HEI scores correlated with the chao index and observed species number primarily in the first trimester (r = 0.25, p < 0.05). Greater carbohydrate intake was associated with a higher abundance of L. crispatus, while lower carbohydrate intake trended towards more L. iners (0.056) and anaerobic species. Conclusions: Increased carbohydrate consumption and improved diet quality may be associated with beneficial vaginal microbial composition in pregnancy. Full article

Lichen-feeding termites occupy a distinctive ecological niche. This feeding behavior underscores a complex interplay between the termites’ digestive abilities and the biochemical properties of lichens, known for their resilience and production of secondary metabolites. Understanding the dietary preferences and digestive mechanisms of these termites offers insights into their ecological roles and the evolutionary adaptations that enable them to exploit such a specialized food source. We conducted experiments with Constrictotermes cyphergaster, feeding it with different combinations of its natural food sources: wood bark and lichen from host trees. Gut microbial communities were analyzed through 16S rRNA sequencing and shotgun metagenomics. Our results revealed that a diet containing lichens induces a shift in microbiota composition and increases the abundance of genes encoding an AA3 enzyme with a role in lignin digestion. This study emphasizes the potential role of lichens in enhancing the digestive capabilities of termites, highlighting the intricate relationships between diet, gut microbiota, and enzymatic activity in Termitidae. Full article

Background: The giant keyhole limpet Megathura crenulata is a gastropod mollusk (Fissurella superfamily) that is endemic to the eastern Pacific coast from southern California, USA, to Baja California Sur, Mexico. M. crenulata is socioeconomically important as it produces a potent immune-stimulating protein, called Keyhole Limpet Hemocyanin, which is extracted in vivo and utilized for vaccine development. However, ecological studies are scarce and genetic knowledge of the species needs to be improved. Our objectives were to assemble and annotate the mitogenome of M. crenulata, and to assess its phylogenetic relationships with other marine gastropods and to evaluate its population genetic diversity and structure. Methods: Samples were collected for mitogenome assembly (n = 3) spanning its geographic range, Puerto Canoas (PCA) and Punta Eugenia (PEU), Mexico, and California (CAL), USA. Total DNA was extracted from gills sequenced using Illumina paired-end 150-bp-read sequencing. Reads were cleaned, trimmed, assembled de novo, and annotated. In addition, 125 samples from eight locations were analyzed for genetic diversity and structure analysis at the 16s rRNA and COX1 genes. Results: The M. crenulata mitogenomes had lengths of 16,788 bp (PCA) and 16,787 bp (PEU) and were composed of 13 protein-coding regions, 22 tRNAs, two rRNAs, and the D-Loop region. In terms of phylogeographic diversity and structure, we found a panmictic population that has experienced recent demographic expansion with low nucleotide diversity (0.002), high haplotypic diversity (0.915), and low φ_ST (0.047). Conclusions: Genetic insights into the giant keyhole limpet provides tools for its management and conservation by delimiting fishing regions with low genetic diversity and/or genetically discrete units. Full article

The search for the microorganisms responsible for sulfide formation and corrosion of steel equipment in the oil fields of Tatarstan (Russia) resulted in the isolation of a new halotolerant strictly anaerobic sulfate-reducing bacterium, strain 5S69^T. The cells were motile curved Gram-negative rods. Optimal growth was observed in the presence of 2.0–4.0% (w/v) NaCl, at pH 6.5, and at 23–28 °C under sulfate-reducing conditions. The isolate was capable of chemoorganotrophic growth with sulfate and other sulfoxides as electron acceptors, resulting in sulfide formation; and of pyruvate fermentation resulting in formation of H₂ and acetate. The strain utilized lactate, pyruvate, ethanol, methanol, fumarate, and fructose, as well as H₂/CO₂/acetate for sulfate reduction. The genome size of the type strain 5S69^T was 4.16 Mb with a G + C content of 63.0 mol%. On the basis of unique physiological properties and results of the 16S rRNA gene-based phylogenetic analysis, phylogenomic analysis of the 120 conserved single copy proteins and genomic indexes (ANI, AAI, and dDDH), assigning the type strain 5S69^T ((VKM B-3653^T = KCTC 25499^T) to a new species within the genus Pseudodesulfovibrio, is suggested, with the proposed name Pseudodesulfovibrio methanolicus sp. nov. Genome analysis of the new isolate showed several genes involved in sulfate reduction and its sulfide-producing potential in oil fields with high saline formation water. Full article

Camelina (Camelina sativa (L.) Crantz) is a valuable source of essential amino acids, especially sulphur-containing ones, which are generally lacking in leguminous crops, thus representing an alternative source of protein for both humans and farm animals. Rhizosphere soil samples from five experimental plots with mono- and mixed cultivations of three camelina cultivars, including two introduced varieties Cs1.Pro (Luna) and Cs2.Pro (Lenka) and one Bulgarian variety Cs3.Pro (local Bulgarian landrace) with variety 666 of vetch (Vicia sativa L.) (Cs3-Vs.Pro) and variety Mir of pea (Pisum sativum L.) (Cs3-Ps.Pro), were collected and analysed. The total DNA was isolated from the rhizosphere soils and the presence of the 16S rRNA gene was confirmed by amplification with the universal primer 16SV34. In the present study, the structure of the soil bacterial community in five different plots (Cs1.S.Pro, Cs2.S.Pro, Cs3.S.Pro, Cs3.Vs.S.Pro, and Cs3.Ps.S.Pro) where camelina was grown alone and by being intercropped with pea and vetch was analysed via a metagenomic approach. The number of observed species was highest in the local genotype of the camelina Cs3 grown alone, followed by soil from the intercropped variants Cs3-Vs and CsS-Ps. The soil bacterial communities differed between the sole cultivation of camelina and that grown with joint cultivation with vetch and peas, indicating that legumes considerably affected the growth and development of beneficial microorganisms by aspects such as nitrogen fixing, levels of nitrifying bacteria, and levels of phosphorus-dissolving bacteria, thus helping to provide better plant nutrition. The α-diversity indicated that bacterial communities in the rhizosphere were higher in soils intercropped with vetch and pea. The optical properties of cereals and legumes were determined by their energy structure, which includes both their occupied and free electronic energy levels and the energy levels of the atomic vibrations of the molecules or the crystal lattice. Full article

This study was to investigate the effects of the polysaccharides (PPM60−III) and sulfated polysaccharides (SPPM60−III) of pine pollen on the Th17/Treg balance, inflammatory cytokines, intestinal microbiota, and metabolite distribution in 3% DSS drinking water-induced UC mice. First of all, the physiological results showed that PPM60−III and SPPM60−III could alleviate UC, which was shown by the reduction in liver Treg cells, the rebalance of Th17/Treg, and the modulation of inflammatory cytokines. In addition, the 16S rRNA results showed that PPM60−III and SPPM60−III could decrease Beijerinck and Bifidobacterium, and increase Akkermansia, Escherichia coli, and Fidobacteria. Finally, the metabonomics results showed that PPM60−III and SPPM60−III also restored purine and glycerolipid metabolism, up-regulated nicotinate and nicotinamide metabolism and caffeine metabolism to inhibit inflammation. In conclusion, PPM60−III and SPPM60−III could inhibit UC by regulating gut bacteria composition and metabolite distribution; SPPM60−III showed better anti-colitis activity. Full article

Sucralose stands as the most common non-nutritive sweetener; however, its metabolic effects have sparked significant controversy over the years. We aim to examine the effects of sucralose daily intake on glycemia, subjective appetite, and gut microbiota (GM) changes in subjects with overweight or obesity. In this randomized, crossover, and controlled trial, 23 participants with a body mass index between 25 kg/m² and 39.9 kg/m² will be assigned to one of two interventions to receive either sucralose (2 mg/kg/day equivalent to 40% of the acceptable daily intake) or glucose (control) for 4 weeks, each phase separated by a 4-week washout period. The glycemic response will be determined during a meal tolerance test, subjective appetite will be evaluated using a visual analog scale, and GM changes will be analyzed by next-generation sequencing of the bacterial rRNA 16S gene from fecal samples. All measures will be performed before and after intervention periods. We hypothesize that sucralose supplementation induces changes in glycemic response, subjective appetite, and gut microbiota in overweight and obese participants. This protocol was approved by the Ethics Committee of the UJAT (No. 0721) and was registered in the Australian New Zealand Clinical Trials Registry (ACTRN12621001531808). Full article

Regular exercise as part of one’s lifestyle is well-recognized for its beneficial effect on several diseases such as cardiovascular disease and obesity; however, many questions remain unanswered regarding the effects of exercise on the gut environment. This study aimed to investigate the impact of long-term endurance exercise on modulating inflammation and endoplasmic reticulum (ER) stress. Fifteen-week-old male Sprague-Dawley (SD) rats were subjected to six months of endurance treadmill training, while age-matched controls remained sedentary. Results showed that IL-6 mRNA levels in colon tissues were significantly higher in the exercise group compared to the sedentary group. Exercise activated a significant ER stress-induced survival pathway by increasing BiP and phosphorylation of eIF2α (p-eIF2α) expressions in the liver and colon, while decreasing CHOP in the liver. Gene expressions of MUC2, Occludin, and Claudin-2 were increased in the colon of the exercise group, indicating enhanced intestinal integrity. Furthermore, the data showed a positive correlation between microbiota α-diversity and BiP (r = 0.464~0.677, p < 0.05). Populations of Desulfovibrio C21 c20 were significantly greater in the exercise group than the sedentary group. Additionally, predicted functions of the gut microbial community in terms of enzymes and pathways supported the enhancement of fatty-acid-related processes by exercise. These findings suggest that prolonged endurance exercise can affect the colon environment, which is likely related to changes in inflammation, ER stress, mucin layers and tight junctions, associated with modifications in the gut microbiome. Full article

The bullfrog Aquarana catesbeiana is one of the main farmed frog species in China, with a low overall survival of farmed bullfrogs from hatching to harvest since bullfrog tadpoles are fragile during the metamorphosis period. The intestinal bacterial community can play crucial roles in animal development; however, little is known about the alteration of the gut microbial community of A. catesbeiana during metamorphosis. The present study used 16S rRNA amplicon sequencing to investigate the intestinal bacterial community in A. catesbeiana at four distinct developmental stages. Moreover, we determined the bullfrog’s body morphological parameters and the intestine histology at different developmental stages. The results showed a reduction in the total length and snout–vent length of A. catesbeiana during metamorphosis. The intestinal microbial composition of A. catesbeiana exhibited variation throughout the process of metamorphosis. The terrestrial stage showed shifts in the bacterial composition compared to the aquatic stages, including a reduction in Bacteroidetes and an increase in Firmicutes. Furthermore, the presence of Prevotella, Bifidobacterium, Leucobacter, Corynebacterium, Bulleidia, Dorea, Robinsoniella, and Clostridium in A. catesbeiana metamorphosis appears to be mainly related to the host’s epithelial cells’ height and total body mass. The results indicated that the intestinal microbial composition changed with the bullfrog–tadpole metamorphosis. The genera of Prevotella, Bifidobacterium, Leucobacter, Corynebacterium, Bulleidia, Dorea, Robinsoniella, and Clostridium might be potential probiotics. Full article

Synthetic culture media, such as Zarrouk’s medium (ZM), are widely used in industrial Arthrospira cultivation but rely heavily on chemical fertilizers, raising concerns over cost and environmental impact. In natural habitats where Arthrospira blooms, the macronutrient concentrations are much lower than those provided by synthetic media. We hypothesized that natural growth may be facilitated by a microbial consortium. To test this, we developed a lab-scale Arthrospira platensis H53 cultivation system using a newly developed organic compost medium (OCM), designed to mimic the natural nutrient composition and microbial interactions. Compared to ZM, A. platensis H53 grown in OCM exhibited elevated growth by day 7. The specific growth rate in OCM was 0.20 day⁻¹, higher than that of 0.17 day⁻¹ in ZM, with optical density values reaching 1.57, compared to 1.13 in ZM. A 1.63-fold increase in biomass was observed in OCM, despite lower initial macronutrient concentrations. Nutrient use efficiency (NUE) in OCM was significantly improved, with nitrate (NO₃⁻) and phosphate (PO₄³⁻) utilization up to 5.8-fold higher. Additionally, A. platensis H53 filaments in OCM were more tightly coiled, indicating a physiological change in response to lowered macronutrient concentrations. Microbial composition analysis using 16S rRNA gene amplicon sequencing revealed the presence of growth-promoting bacteria, including Pontibacter spp., Brevundimonas spp., and Aliihoeflea spp., likely contributing to nutrient cycling and enhanced growth. These findings suggest potential symbiotic interactions between cyanobacteria and non-cyanobacteria in the OCM system, promoting increased growth and productivity. This study is the first to propose such symbiosis in an extremely alkalophilic environment, offering another sustainable alternative to traditional chemical-based Arthrospira cultivation methods. Full article

Background/Objectives: The phyla Firmicutes and Bacteroidetes are the main constituents of the gut microbiota. An imbalance in the gut microbiota is a sign of dysbiosis, and the Firmicutes-to-Bacteroidetes ratio has been proposed to be a marker of it, especially in the context of obesity. Since Croatia is the country with one of the highest obesity rates in Europe, a pilot observational study was conducted. The aim of the study was to investigate the validity of this potential biomarker in a methodological study using sample processing, DNA sequence analysis and characterization of recruited participants, including various health factors. Methods: A study involving Croatian population was conducted. Participants age, body weight, gender, health history and lifestyle factors were recorded. Gut microbiota composition was analyzed using 16S rRNA sequencing. The F/B ratio was calculated and evaluated in the context of health factors. Statistical analysis was performed to detect the possible association of F/B ratio and excess body weight (kg) and possible impact of certain lifestyle factors. Results: No association between the F/B ratio and excess body weight (kg) was found. Excess body weight was significantly associated with higher age, male gender, and history of appendectomy. No significant health predictors of the F/B ratio were found, but weight gain was positively associated with a higher average F/B ratio. Conclusions: Although this study could not confirm the predictive value of the F/B ratio or any other phyla-related biomarker for excess body weight in the study population, it demonstrated interesting insights into the obesity-associated gut microbiota. Full article

Subtropical moss peatlands have important ecological functions, and their protection and restoration are urgent. The lack of understanding of the biogeochemical changes in subtropical moss peatlands after human disturbance, particularly regarding their underground ecological changes, limits the efforts towards their protection and restoration. In this study, typical subtropical moss peatlands and the Cryptomeria swamp forest (CSF) formed by long-term (more than 20 years) drainage and afforestation in the Yunnan–Guizhou Plateau of China were selected as the research sites. Moreover, 16S rRNA high-throughput sequencing technology was used to study the differences in soil bacterial community diversity and composition among a natural Sphagnum fen (SF), Polytrichum bog (PB), and CSF to explore the effects of drainage and afforestation on different types of moss peatlands and its mechanism combined with soil physicochemical properties. Results showed that (1) drainage and afforestation significantly reduced the α diversity of soil bacterial communities in SF while significantly increasing the α diversity of soil bacterial communities in PB. Soil bacterial communities of SF had the highest α diversity and had many unique species or groups at different taxonomic levels. (2) The impact of drainage and afforestation on the soil bacterial community composition in SF was significantly higher than that in PB. Drainage and afforestation caused significant changes in the composition and relative abundance of dominant groups of soil bacteria in SF at different taxonomic levels, such as significantly reducing the relative abundance of Proteobacteria, significantly increasing the relative abundance of Acidobacteria, and significantly reducing the ratio of Proteobacteria to Acidobacteria, but did not have a significant impact on the corresponding indicators of PB. The changes in the ratio of Proteobacteria to Acidobacteria may reflect changes in the trophic conditions of peatlands. (3) Soil moisture content, available phosphorus content, and pH were key driving factors for changes in soil bacterial community composition and diversity, which should be paid attention to in the restoration of moss peatlands. This study provides insights into the protection and restoration of subtropical moss peatlands. Full article

Ciliated microeukaryotes are insufficiently investigated despite their ubiquity and ecological significance. The morphology and morphogenesis of a new Stichotrichida species, Pseudosincirra binaria sp. nov., and the known Perisincirra paucicirrata Foissner et al., 2002, are here studied using live observations and protargol staining methods. The new species is characterized by having one buccal, one parabuccal and three frontal cirri, one frontoventral row extending to the posterior half of the cell, three left and two right marginal rows and three dorsal kineties with the left kinety conspicuously bipartite, along with one caudal cirrus at the rear end of each kinety. During morphogenesis, there exist five frontal-ventral cirral anlagen with anlagen IV and V forming a frontoventral row in the proter, and four cirral anlagen with only anlage IV generating a frontoventral row in the opisthe. The anlagen for marginal rows and dorsal kineties develop intrakinetally. The new population of Perisincirra paucicirrata corresponds well with other isolates regarding morphology and cell development. Phylogenetic analyses based on small subunit ribosomal gene sequence data revealed that both Perisincirra and Pseudosincirra are deeply clustered in the clade consisting of species from the genera Deviata and Heterodeviata, supporting the placement of both genera into the family Deviatidae Foissner, 2016. Full article