16S rRNA Gene Sequence Research Articles

Modulation of Gut Microbiota Composition and Microbial Phenolic Catabolism of Phenolic Compounds from Achillea millefolium L. and Origanum majorana L.

The impact of the nonbioaccessible fraction of two phenolic-rich extracts from Achillea millefolium L. (yarrow) and Origanum majorana L. (marjoram) on the modulation of the human gut microbiota was investigated in vitro. Microbial metabolism of the phenolic compounds was also addressed. In general, phenolic acids or O-glycosidic flavones quickly disappeared, in contrast to methoxy- or C-glycosidic flavonoids. This colonic metabolism yielded phloroglucinol, 3,4-dimethoxyphenylacetic acid, 3-(4-hydroxyphenyl)-propionic acid, and 4-hydroxybenzoic acid as the main metabolites of the microbial catabolism of rosmarinic acid or caffeoylquinic acids, among others. The 16S rRNA gene sequencing showed that the most promising modulatory effect was related to the increase in Bifidobacterium spp., Collinsella spp., Romboutsia, and Akkermansia muciniphila for both plant extracts, along with Blautia spp. and Dialister for yarrow extract. This beneficial modulation was accompanied by the increase in butyric acid production, highlighting the potential prebiotic-like effect on the gut microbiota of these two previously unstudied edible plants.

The role of gut microbiota and metabolomic pathways in modulating the efficacy of SSRIs for major depressive disorder

This study aims to explore the mechanism by which gut microbiota influences the antidepressant effects of serotonin reuptake inhibitors (SSRIs) through metabolic pathways. A total of 126 patients were analyzed for their gut microbiota and metabolomics. Patients received SSRI treatment and were categorized into responder and non-responder groups based on changes in their Hamilton Depression Rating Scale (HAMD-17) scores before and after treatment. The association between gut microbiota composition and the efficacy of SSRIs was investigated through 16S rRNA gene sequencing and metabolomic analysis, and a predictive model was developed. As a result, the study found significant differences in gut microbiota composition between the responder and resistant groups. Specific taxa, such as Ruminococcus, Bifidobacterium, and Faecalibacterium, were more abundant in the responder group. Functional analysis revealed upregulation of acetate degradation and neurotransmitter synthesis pathways in the responder group. The machine learning model indicated that gut microbiota and metabolites are potential biomarkers for predicting SSRIs efficacy. In conclusion, gut microbiota influences the antidepressant effects of SSRIs through metabolic pathways. The diversity and function of gut microbiota can serve as biomarkers for predicting the treatment response, providing new insights for personalized treatment.

Bacteriovorax antarcticus sp. nov., a bacterial predator isolated from near Potter Cove on King George Island, Antarctica.

A new species of bacterial predator (PP10T) was isolated from a biocrust sample taken from near Potter Cove, King George Island, Antarctica (62°14'15.62″S 58°43'15.65″W). The Bdellovibrio and like organism was vibrio-shaped and employed a single polar flagellum for motility. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that this isolate clustered within the genus Bacteriovorax in the family Bacteriovoracaceae. The 16S rRNA gene sequence similarities between isolate PP10T and the type strain (Bacteriovorax stolpii DSM 12778T) were only 97.14%. The draft genome of PP10T has a size of 4.243 Mbps, with 4148 genes and a G+C content of 38.49%. While the optimal temperature for its growth was 25 °C, PP10T was active at 4 °C, classifying it as psychrotolerant. The results of genetic and physiological tests indicated phenotypic differentiation of strain PP10T from the type strain Bx. stolpii DSM 12778T. Based on physiological and phylogenetic analyses, as well as the prey spectrum, isolate PP10 represents a novel species within the genus Bacteriovorax, for which the name Bacteriovorax antarcticus sp. nov. is proposed. The type strain is PP10T (= KCTC 8097T = DSM 116241T).

Fucoidan-Mediated Covalent Modification Mitigates Allergenicity of Shrimp (Penaeus vannamei) in Mice via Enhanced Intestinal Barrier Function and Antigen Presentation Suppression.

Covalent modification is an effective strategy for reducing the allergenicity of single allergens. However, due to the complexity of the food matrix, its application in hypoallergenic food production requires further exploration. The study showed that covalent modification of fucoidan decreased the specific antibody levels, inhibited Th2 cell differentiation, and reduced mast cell degranulation, suggesting that it significantly reduced the allergenicity of Penaeus vannamei. Further analysis showed that covalent modification not only up-regulated the intestinal tight junction proteins expression and improved intestinal mucus secretion but also restored intestinal microbial homeostasis by immunological and 16S rRNA gene sequencing. Additionally, covalent modification inhibited dendritic cell maturation and CD8+ T cell differentiation, thereby reducing antigen recognition and presentation, as determined by transcriptome and flow cytometry. Therefore, the covalent modification of fucoidan reduced shrimp allergenicity by enhancing intestinal barrier function and inhibiting antigen presentation. In conclusion, it is a potential strategy for processing hypoallergenic foods.

Promoting the recovery of soil health in As and Sb-polluted soils: new evidence from the biochar-compost option.

The role of compost and biochar in the recovery of As and Sb-polluted soils is poorly investigated, as well as the influence of their application rates on soil health and quality. In this study, we therefore investigated the effectiveness over time (2, 4, and 6months, M) of a municipal solid waste compost (MSWC) and a biochar (BC), applied at 10 and 30% rates, and of selected mixtures (MIX; applied at 10 and 30% total rates, 1:1 ratio of MSWC and BC), on labile As and Sb in a polluted soil from an abandoned Sb mine (Djebel Hamimat, Algeria). At the same timepoints, the amendment impact on soil chemistry was also monitored, while the activity and diversity of the resident microbial communities were investigated at 6M. After 6months, MSWC, BC, and MIX applied at the higher rate significantly increased soil pH (from 7.5 up to 8.2), while MSWC and MIX increased soil EC to worrying values. The soil dissolved organic carbon content was also greatly increased by MSWC and MIX at the higher rates (up to 50-fold), while BC showed a negligible impact. All the amendments reduced the concentration of labile Sb in soil, with BC 10% being the most effective treatment (i.e., reducing labile Sb from ~ 60 to 20mgkg-1 soil). On the contrary, only BC and MIX applied at 10% significantly reduced labile As (e.g., from ~ 12 to 4mgkg-1 soil in the case of BC). MSWC and MIX at both rates increased up to 2000-fold soil dehydrogenase activity, while BC showed a null impact. The Biolog community level physiological profile and sequencing of the partial 16S rRNA gene showed a reduction of catabolic activity and α-diversity and a change of the community composition of bacterial populations in treated soils. Overall, MIX treatment, especially at 10%, was the most promising option for the chemical and biological recovery of As and Sb-polluted soils.

Molecular Characterization of Streptococcus spp. Isolated from Milk, Feces and Farm Environment of Mastitic Dairy Cows

Streptococci are the primary cause of mastitis, significantly impacting the dairy industry economically. This study aimed to explore the molecular epidemiology, antimicrobial resistance, and virulence characteristics of Streptococcus spp. isolated from the milk, feces, and environment of dairy cows with mastitis. Sixty (60) samples (milk = 20, feces = 20 and soil = 20) from cows with clinical mastitis (CM) were purposively collected and examined. Samples were enriched in Luria Bertani broth (LB) and Streptococcus spp. was isolated on Modified Edwards Medium and confirmed by ribosomal (16S rRNA) gene sequencing. Twenty-two (36.67%) of the samples were positive for Streptococcus spp. (milk = 40.90%, feces = 31.82% and soil = 27.28%) by cultural and molecular examination. Phylogenetic analysis revealed 59.5, 30.5, 6.0% and 4.0 % of the Streptococcus isolates as S. uberis, S. agalactiae, S. hyovaginalis and S. urinalis, respectively. The milk samples had higher prevalence (42.75%) of S. uberis mastitis than feces (36.80%) and soil (20.45%) samples. Likewise, S. agalactiae was prevalent in 51.5%, 37.60% and 10.90% milk, feces and soil samples, respectively. The draft assembly sizes of G2M6 and G6M1 were 1,960,858 and 2,303,841 base pair (bp), respectively. The strains were typed as S. uberis sequence type 155 (ST155) and S. agalactiae sequence type 58 (ST58). The G2M6 genome contained 367 SEED subsystem features, 45 antimicrobial resistance genes (ARGs), and 160 virulence and virulence-related genes, whereas the G6M1 genome possessed 378 SEED subsystem features, 41 ARGs and 178 virulence genes. One plasmid replicon such as IncY of 4,012 bp, was identified in the G6M1 genome (with 95% identity and 60% coverage) while G2M6 genome harbored none. Genome completeness analysis using BUSCO revealed the presence of 100% complete BUSCOs in the hybrid assembly of both genomes. Streptococcus spp. associated with bovine mastitis exhibit a variety of genomic traits and harbor an array of ARGs and virulence genes. Further investigation is needed to identify specific traits that govern virulence fitness in the pathophysiology of mastitis. J. of Sci. and Tech. Res. 6(1): 01-12, 2024

Microbial profiling of the East Siberian Sea sediments using 16S rRNA gene and metagenome sequencing

The Arctic Ocean is experiencing significant global warming, leading to reduced sea-ice cover, submarine permafrost thawing, and increased river discharge. The East Siberian Sea (ESS) undergoes more significant terrestrial inflow from coastal erosion and river runoff than other Arctic seas. Despite extensive research on environmental changes, microbial communities and their functions in the ESS, which are closely related to environmental conditions, remain largely unexplored. Here, we investigated microbial communities in ESS surface sediments spanning latitudes from 73°N to 77°N using 16S rRNA amplicon sequencing, and reconstructed 211 metagenome-assembled genomes (MAGs) using shotgun metagenome sequencing. Taxonomic analysis identified 209 bacterial MAGs, with the predominant phyla Pseudomonadota (n = 82), Actinobacteriota (n = 38), Desulfobacterota (n = 23), along with 2 archaeal MAGs of Thermoproteota. Notably, 86% of the MAGs (n = 183) could not be classified into known species, indicating the potential presence of novel and unidentified microorganisms in the ESS. This dataset provides invaluable information on the microbial diversity and ecological functions in the rapidly changing ESS.

The impact of interactions between heavy metals and smoking exposures on the formation of oral microbial communities

IntroductionThe primary objective of our investigation was to assess the repercussions of prolonged exposure to heavy metals and smoking on the microbiome of the oral buccal mucosa. Concurrently, we aimed to elucidate the intricate interplay between external environmental exposures and the composition of the oral microbial ecosystem, thereby discerning its potential implications for human health.MethodsOur study cohort was stratified into four distinct groups: MS (characterized by concurrent exposure to heavy metals and smoking), M (exposed solely to heavy metals), S (exposed solely to smoking), and C (comprising individuals serving as a control group). Specimens of buccal mucosa and blood were systematically acquired from the participants, facilitating subsequent microbial diversity analysis across the four oral buccal mucosa sample cohorts through 16S rRNA gene sequencing techniques. Simultaneously, blood samples were tested for heavy metal concentrations. In addition, we performed topological analyses by constructing microbial networks.ResultsOur findings notably indicate that co-exposure to heavy metals and smoking yielded a more pronounced alteration in the diversity of oral microflora when compared to singular exposures to either heavy metals or smoking. By comparing the oral bacterial communities and functional pathways between the four groups, we found significant differences in bacterial communities and functional pathways between the groups. Notably, the impact of heavy metal exposure overshadowed that of smoking, with concurrent exposure to heavy metals and smoking eliciting marginally greater effects than exposure to heavy metals alone. In addition, our analysis of the correlation between microbiota and blood heavy metal concentrations showed that the heavy metal cadmium (Cd) had a significantly greater effect on oral microbiota than other heavy metals.DiscussionChronic exposure to heavy metals and smoking disrupts the normal bacterial communities in the oral mucosa of residents of contaminated areas. This exposure reduces the complexity and stability of microbial networks and increases the risk of various diseases reduces the complexity and stability.

The Effect of Gender on the Intestinal Flora of Colorectal Cancer Under Different Stages.

This study aims to determine whether gender is a factor in the interplay between the human intestinal flora and colorectal cancer (CRC), ultimately providing new evidence for the clinical prediction and management of CRC in different genders. In this study, we included 186 untreated CRC patients, and classified them into two groups based on pathological staging: Groups Ⅰ-Ⅱ and Groups Ⅲ-Ⅳ, with male and female groups within each group. We collected preoperative fecal samples from these patients and performed 16S rRNA gene sequencing to analyze their intestinal flora. In the CRC Stages I-II cohort, the gut microbiota of the female group exhibited greater diversity and abundance compared to the male group, with a total of 13 gut microbiota demonstrating significant disparities. Notably, s__Parabacteroides gordonii, s__Bacteroides faecis, and s__Bacteroides nordii were found to be more prevalent in the female group relative to the male group. Within the CRC Stages III-IV cohort, 51 gut microbiota exhibited significant differences between the genders. In the immunocyte composition of fecal samples from patients with CRC, a higher proportion of naive B cells is observed in the male group as compared to the female group. In female CRC patients within the CRC Stages III-IV cohort, Actinomyces exhibited a significant negative correlation with activated dendritic cells, CD4+ memory T cells, and eosinophils. In male CRC patients within the CRC Stages III-IV cohort, Actinomyces demonstrated a significant positive correlation with naive B cells and a significant positive correlation with immune activation genes TNFRSF25 and TMIGD2. In female CRC patients within the CRC Stages III-IV cohort, Actinomyces showed a significant negative correlation with activated dendritic cells, CD4+ memory T cells, and eosinophils, and a significant positive correlation with immune activation genes TNFSF13B, LTA, KLRK1, and CXCL12. In the CRC Stages I-II group, the female group's intestinal flora is more diverse and richer than the male group. In the CRC Stages III-IV group, there are a total of 51 different intestinal flora in both the male and female groups. We also found that Actinomyces affects the occurrence and development of CRC in the male and female groups through different pathways. The results show that the intestinal flora differs between male and female CRC patients and is closely associated with cancer development.

Segatella asaccharophila sp. nov., an anaerobic pectinophile isolated from a two-phase methane fermentation system.

An obligately anaerobic, Gram-stain-negative, non-spore-forming and non-motile rod (strain LPYR103-PreT) was isolated from a two-phase methane fermentation system. Using 16S rRNA gene sequence-based phylogenetic analysis, strain LPYR103-PreT was classified in the genus Segatella. The 16S rRNA gene sequence similarity, average nucleotide identity and digital DNA-DNA hybridization between strain LPYR103-PreT and its phylogenetically nearest species - Segatella cerevisiae JCM 30867T - were 94.4, 77.9 and 23.4%, respectively. The genome size of strain LPYR103-PreT was 3 326 733 bp, and its genomic DNA G+C content was 44.05%. The most abundant cellular fatty acid was anteiso-C15 : 0. The growth of strain LPYR103-PreT was stimulated by the addition of pectin, d-galacturonate and d-glucuronate; in contrast, the strain exhibited poor growth in the presence of common sugars, such as glucose. Therefore, strain LPYR103-PreT was classified as a pectinophile - a bacterium that shows a preference for pectin and a few related compounds as substrates. Glucose is degraded by type strains of 12 species belonging to the genus Segatella; thus, strain LPYR103-PreT is the first described pectinophile belonging to this genus. Strain LPYR103-PreT produced succinate and acetate as its major metabolic end products. Based on the differences in the phylogenetic, genomic, physiological and chemotaxonomic characteristics of strain LPYR103-PreT and related species, the name Segatella asaccharophila sp. nov. is proposed to accommodate strain LPYR103-PreT (= NRIC 0997T = JCM 37351T=DSM 118531T = KCTC 25923T).

Sphingomonas longa sp. nov., Sphingomonas mollis sp. nov. and Sphingomonas aurea sp. nov.: three novel Sphingomonas species isolated from soil.

Three Gram-negative, aerobic and non-motile bacterial strains, BT552T, BT553T and KR1UV-12T, were isolated from soil samples in Gwangju-si and Gangneung-si, the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequence showed that strains BT552T, BT553T and KR1UV-12T clustered to a distinct clade within the family Sphingomonadaceae (order Sphingomonadales, class Alphaproteobacteria). The strains exhibited the highest genetic similarity with representatives of the genus Sphingomonas; moreover, strains BT552T and BT553T tightly clustered with Sphingomonas melonis DAPP-PG 224T (98.2 and 98.1 %) and Sphingomonas aquatilis JSS-7T (98.1 and 98.0 %), while strain KR1UV-12T clustered with S. melonis DAPP-PG 224T (97.9%) and Sphingomonas rubra BH3T (97.8%), respectively. The major cellular fatty acids of all three strains were summed feature 8 (C18:1 ω7c/C18:1 ω6c), comprising 44.7, 46.4 and 48.5%. Additionally, their respiratory quinone is Q-10, and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids, sphingolipid and phosphatidylcholine. They all grow well at an optimum temperature of 25 °C, at pH 7. The draft genomes of strains BT552T, BT553T and KR1UV-12T measures 4 035 561 bp, 3 941 714 bp and 3 418 792 bp, respectively, comprising 3 804 3648 and 3236 coding sequences and 50, 48 and 45 RNA genes. The average nucleotide identity analysis and digital DNA-DNA hybridization values between BT552T, BT553T and KR1UV-12T and closely related Sphingomonas species range from 72.7 to 80.2% and 19.4 to 24.3%, respectively. Based on phenotypic, genotypic and chemotaxonomic data, these three strains BT552T, BT553T and KR1UV-12T represent three novel bacterial species within the genus Sphingomonas for which the names Sphingomonas longa sp. nov. (type strain BT552T= KCTC 82094T =NBRC 114993T), Sphingomonas mollis sp. nov. (type strain BT553T =KCTC 82095T =NBRC 114994T) and Sphingomonas aurea sp. nov. (type strain KR1UV-12T = KCTC 92959T = TBRC 18506T) are proposed.

Quantitative real-time PCR analysis of gut microbiota in rheumatoid arthritis patients compared to healthy controls

Rheumatoid arthritis (RA) is an autoimmune disorder with synovial inflammation of joints and extra articular manifestations. The results of recent researches consider the relationship between microbiota and the immune system as a double-edged sword. Considering that the relationship between the composition of intestinal microbiota and the immunological and clinical status of the body has been confirmed, it is very important to investigate the effect of each genus and species of bacteria on the state of the immune system. The current study was determined using 16S rRNA gene sequencing to explore the 4 selected gut microbiota from 25 people suffering from rheumatism (RA group) with a time interval of at least 3 years from the onset of the disease and 25 Healthy people by real time PCR. Gut dysbiosis in patients with rheumatoid arthritis (RA) is identified alongside key serological and clinical markers such as C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), immunofluorescence (IF), anti-cyclic citrullinated peptide (Anti-CCP), white blood cell count (WBC), mean corpuscular volume (MCV), aspartate aminotransferase (AST), alanine aminotransferase (ALT), blood urea nitrogen (BUN), Platelet count (PLT), thyroid-stimulating hormone (TSH), creatinine (Cr), and hemoglobin (Hb). Additionally, data from individuals with incomplete or unverified records were excluded from the study to ensure accuracy and reliability. Bacteroides fragilis, Roseburia faecis and Fusobacterium nucleatum genera showed a much lower median in Rheumatoid arthritis patients in comparison with healthy people (P > 0.001, p = 0.002, P < 0.001 respectively). While the difference in the median of E. coli genera was not significant in the two studied groups (p = 0.31). In such a way that the change in the Gut normal flora homeostasis and the reduction of beneficial bacteria such as Bacteroides fragilis, Roseburia faecis, Fusobacterium nucleatum genera, may stimulate the immune system to initiate autoimmunity.

Bengtsoniella intestinalis gen. nov., sp. nov., a member of the family Oscillospiraceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus.

A Gram-stain-negative, non-spore-forming, rod-shaped, obligately anaerobic bacterium, designated strain BP47G, was isolated from the hindgut of a silver drummer (Kyphosus sydneyanus) fish collected from the Hauraki Gulf, New Zealand. Phylogenetic analysis based on the 16S rRNA gene sequence of the isolate indicated that it belonged to the family Oscillospiraceae in the phylum Bacillota. The gene sequence of BP47G was most similar to Oscillibacter valericigenes with 95.23% sequence identity. Isolate BP47G grew on agar medium containing mannitol and fish gut fluid as the sole carbon sources. Clear colonies of ~1 mm diameter grew within a week at 20-28 °C (optimum 28 °C) and pH 7.1-8.5 (optimum 8.5). BP47G tolerated the addition to the medium of up to 1% NaCl. Formate and butyrate were the major fermentation products. The major cellular fatty acids were C12:0, C13:0, iso-C14:0, C16:0 and C16:1 cis 7. Genomic analyses comparing BP47G with its closest relatives indicated low genomic relatedness based on the average nucleotide identity, average amino acid identity, percentage of conserved protein and in silico DNA-DNA hybridization. Supported by the phenotypic and taxonomic characteristics observed in this study, a novel genus and species Bengtsoniella intestinalis gen. nov., sp. nov. is proposed for isolate BP47G (=ICMP 24688=JCM 35770).

Diversity and Bioactivities of Ulleung Island-Derived Marine Actinomycetes

Actinomycetes are key producers of bioactive secondary metabolites. In this study, sediment samples were collected using a grab sampler from the coast of Ulleung Island and inoculated on various agar media by stamping to isolate Actinomycetes. As a result, 69 Actinomycete strains were isolated and laboratory-cultured from the sediment samples. The isolates were assigned to the genera Streptomyces (44 strains), Nocardia (6 strains), Rhodococcus (6 strains), Mycobacterium (6 strains), Micromonospora (3 strains), Nocardioides (2 strains), Marmoricola (1 strain), and Oerskovia (1 strain) based on 16S rRNA gene sequence analysis. The antibacterial activity and potential toxicity of the culture broth extracts were tested for all isolates. Extracts from some strains exhibited strong antibacterial activity against Acinetobacter baumannii 04 and methicillin-resistant Staphylococcus aureus. Additionally, some extracts were toxic to brine shrimp. This study confirms that marine Actinomycetes from Ulleung Island encompass unique and diverse taxonomic groups and are a good source of bioactive natural products.

Long-term adaptation to dietary shifts of gut microbiota in gilthead seabream (Sparus aurata)

In many meta-analyses and literature reviews on fish microbiota, the provenance of the animals (farmed vs. wild) is often overlooked. Given the well-established role of diet as a key factor in shaping gut microbiota, this study investigates the impact of dietary nature by comparing the microbiota of gilthead seabream (Sparus aurata) fed a commercial diet versus a wild-type diet, all reared within a recirculating aquaculture system. Over a 60-day period, we tracked changes in gut bacterial diversity, structure, and composition following a shift from a commercial feed to a diet exclusively based on pink shrimp (Parapenaeus longirostris). Gut bacterial communities were assessed using 16S rRNA gene sequencing (Illumina MiSeq platform) with primers targeting the V3-V4 hypervariable regions. Twenty days after the dietary change, microbial diversity (Shannon index) increased in fish fed the shrimp diet compared to those fed the commercial diet, while Dominance index values decreased. Additionally, inter-individual (beta-) diversity based on Bray-Curtis distances also differed between dietary treatments. These results support further that microbiota comparisons between farmed/captive and wild fish are challenging due to the unpredictable feeding regimes and dietary variations in wild fish. However, the diet impact on microbiota diminished over time, with the differences in intra- and inter-individual diversity being reduced after 40 days, which suggests an adaptation of microbial communities to dietary changes. At this point, gut microbial communities also showed a similar taxonomical composition. Moreover, a core microbiota consisting of species belonging to the genera Ralstonia, Paraburkholderia, Fulvimonas, Pseudomonas, and Cutibacterium was maintained in all sampling times under both dietary treatments. Overall, this study serves as a conceptual approach that shows a long-term adaptation of the gut microbiota after a radical dietary change, probably driven by host-inherent factors. Furthermore, these results may be a valuable insight for feed manufacturers aiming to develop sustainable and cost-effective ingredients since they suggest that some alternative feeds and ingredients do not have adverse long-term effects on fish gut microbiota.

The role of anthropogenic influences on a tropical lake ecosystem and its surrounding catchment: a case study of Lake Sentani.

Lake Sentani is a tropical lake in Indonesia, consisting of four interconnected sub-basins of different water depths. While previous work has highlighted the impact of catchment composition on biogeochemical processes in Lake Sentani, little is currently known about the microbiological characteristics across this unique ecosystem. With recent population growth in this historically rural area, the anthropogenic impact on Lake Sentani and hence its microbial life is also increasing. Therefore, we aimed to explore the influence of environmental and anthropogenic factors on the microbial diversity of Lake Sentani. Here we present a detailed microbiological evaluation of Lake Sentani, analyzing 49 different sites across the lake, its tributary rivers and their river mouths to assess diversity and community structure using 16S rRNA gene sequencing. Our results reveal distinct communities in lake and river sediments, supporting the observed geochemical differences. Taxonomic assessment showed the potential impact of anthropogenic pressure along the northern, urbanized shore, as river and river mouth samples revealed high abundances of Bacteroidota, Firmicutes and Cyanobacteria, which could be attributed to pollution and eutriphication. In contrast, lake sediment communities were dominated by Thermodesulfovibrionia, Methanomethylicia, Bathyarchaeia and Thermoplasmata, suggesting sulfate reducing, thermophilic, acidophilic bacteria and methanogenic archaea to play an important role in tropical lake systems. This study provides novel insights into ecological functions of tropical lakes and contributes to the optimization of management strategies of Lake Sentani, ensuring its holistic preservation in the future.

The Microbial Diversity and Traceability Analysis of Raw Milk from Buffalo Farms at Different Management Ranks in Guangxi Province

Farm management has a significant impact on microbial composition and may affect the quality of raw buffalo milk. This study involved a diversity analysis and traceability of the microbial communities in raw buffalo milk from three buffalo farms at different management ranks in Guangxi Province, China. The microbial composition of the raw buffalo milk and its environmental sources were investigated using 16S rRNA gene sequencing and bioinformatics analysis. The results demonstrated that different management ranks significantly influenced microbial composition in milk, with the primary sources of contamination varying across farms. The env.OPS_17 was the predominant differential bacterium in farm rank A, whereas Enterobacteriaceae, Aerococcaceae, and Planococcaceae were dominant in farm rank B. The Fast Expectation–Maximization for Microbial Source Tracking model revealed that while the sources of microbial contamination varied across farms at different management ranks, the teat and teat liner consistently emerged as the primary sources of microbial contamination in raw buffalo milk. This study provides important insights into how different farm management ranks affect the microbial composition of raw buffalo milk, highlighting the importance of improved management practices during milk production, particularly in cleaning the milking equipment and farm environment, as these are key factors in ensuring the quality and safety of raw buffalo milk.

Exploring Novel Fungal–Bacterial Consortia for Enhanced Petroleum Hydrocarbon Degradation

Bioremediation, involving the strategic use of microorganisms, has proven to be a cost-effective alternative for restoring areas impacted by persistent contaminants such as polycyclic aromatic hydrocarbons (PAHs). In this context, the aim of this study was to explore hydrocarbon-degrading microbial consortia by prospecting native species from soils contaminated with blends of diesel and biodiesel (20% biodiesel/80% diesel). After enrichment in a minimal medium containing diesel oil as the sole carbon source and based on 16S rRNA, Calmodulin and β-tubulin gene sequencing, seven fungi and 12 bacteria were identified. The drop collapse test indicated that all fungal and four bacterial strains were capable of producing biosurfactants with a surface tension reduction of ≥20%. Quantitative analysis of extracellular laccase production revealed superior enzyme activity among the bacterial strains, particularly for Stenotrophomonas maltophilia P05R11. Following antagonistic testing, four compatible consortia were formulated. The degradation analysis of PAHs and TPH (C5–C40) present in diesel oil revealed a significantly higher degradation capacity for the consortia compared to isolated strains. The best results were observed for a mixed bacterial-fungal consortium, composed of Trichoderma koningiopsis P05R2, Serratia marcescens P10R19 and Burkholderia cepacia P05R9, with a degradation spectrum of ≥91% for all eleven PAHs analyzed, removing 93.61% of total PAHs, and 93.52% of TPH (C5–C40). Furthermore, this study presents the first report of T. koningiopsis as a candidate for bioremediation of petroleum hydrocarbons.

Metabarcoding analysis of oral microbiome during pregnancy

Pregnancy is a dynamic physiological process involving significant hormonal, immune, and metabolic changes to support fetal growth and development. This study investigates the changes in salivary microbiome and biochemical markers from the second to the third trimester of pregnancy. Saliva samples were collected from 45 pregnant women enrolled in the Qatar Birth Cohort study at two time points (second and third trimesters). DNA was extracted and subjected to 16S rRNA gene sequencing using Oxford Nanopore Technology. Microbial diversity and taxonomic analyses were performed, along with correlation analyses between microbial abundance and clinical parameters. Biochemically, significant increases in BMI, pulse rate, HbA1c, LDL, total cholesterol, and triglycerides were observed in the third trimester compared to the second. Microbial diversity analysis revealed significant changes in microbial richness and composition. Taxonomy analysis showed a significant 3-fold increase in Bacteroidota. Also, a significant decline in Selenomonas and a significant increase in Veillonella, specifically Veillonella dispar and Veillonella atypica, as well as an increase in Granulicatella were observed in the third trimester, along with a significant decrease in Streptococcus sanguinis. Correlation analysis during the second trimester revealed positive associations between BMI, cholesterol, LDL, and Selenomonas, and negative correlations with Streptococcus and Gemella. In the third trimester, BMI was negatively correlated with Campylobacter, glucose levels were negatively correlated with Neisseria, and triglyceride levels were negatively correlated with Prevotella. These findings highlight significant biochemical and microbial shifts during pregnancy, underscoring the importance of monitoring oral health and metabolic changes in pregnant women.

Dynamic Impact of One-Year Integrated Rice–Crayfish Farming on Bacterioplankton Communities in Paddy Water

As global food security issues become increasingly severe, an important innovation in agricultural production patterns, namely integrated rice–fish farming, has been widely implemented around the world, especially in Asia. To assess the impact of integrated rice–crayfish (Procambarus clarkii) farming (IRCF) on agricultural ecosystems, we used Illumina high-throughput 16S rRNA gene sequencing to analyze differences in diversity, composition, co-occurrence network, and assembly process of planktonic bacterial communities in paddy water between traditional rice farming (TRM) and IRCF. Environmental factors and planktonic bacterial communities were evaluated during the tillering, jointing, flowering, and grain-filling stages on August 24, September 5, September 24, and October 16, respectively. Our findings revealed that, throughout the entire cultivation period, IRCF had no notable impacts on bacterioplankton community diversity in paddy water, but it changed the composition and relative abundance of the dominant bacterioplankton. Specifically, IRCF promoted the Chloroflexota during the tillering stage but reduced its presence during the grain-filling stage. It also significantly decreased the Bacillota during the jointing stage while notably enhancing Actinomycetota during the flowering stage. Furthermore, IRCF markedly improved the robustness and negative/positive cohesion within bacterioplankton co-occurrence networks during jointing and grain-filling stages. IRCF altered the assembly processes shaping planktonic bacterial communities, promoting a greater dominance of stochastic processes during the tillering, jointing, and flowering stages and a diminished dominance during the grain-filling stage. IRCF dramatically changed aquatic environmental factors, particularly during the jointing stage, by substantially increasing the TN, ammonium, nitrate, and phosphate levels in paddy water. These nutrient levels were closely correlated with the dynamics of the planktonic bacterial communities. Our findings underscore the considerable potential of IRCF in enhancing the stability of bacterioplankton communities and promoting rice growth while also providing valuable data and theoretical insights into the microbiological ecological impacts of IRCF on the agroecosystem.