16S rRNA Gene Research Articles

Miao sour soup alleviates DSS-induced colitis in mice: modulation of gut microbiota and intestinal barrier function.

Miao sour soup (MSS), a daily fermented food in Guizhou, China, is rich in microorganisms with various beneficial activities, including anti-inflammatory and antioxidant activities. However, the therapeutic effects of MSS on IBD remain unexplored. This study aimed to investigate the protective effect of MSS against colitis in mice. In this study, we examined the microbial community structure of MSS by metagenomic sequencing and also explored the protective effect of MSS on DSS-induced colitis in mice. We investigated the effects of MSS on intestinal inflammatory response and intestinal barrier function in mice. Finally, the changes in intestinal flora were analyzed based on the 16S rRNA gene sequencing results. Significantly, the experiment result shows that MSS ameliorated the severity of DSS-induced disease in mice by mitigating colitis-associated weight loss, reducing the disease activity index of IBD, alleviating colonic hemorrhagic lesions, increasing colon length, and improving colonic tissue damage. Moreover, MSS preserved intestinal barrier integrity and restored intestinal epithelial function in mice. Additionally, MSS modulated the structure and composition of the intestinal flora. Furthermore, MSS downregulated pro-inflammatory factors and attenuated the NF-κB p65 expression, thereby mitigating the inflammatory response. These findings highlight the protective effect of MSS against DSS-induced colitis, providing substantial scientific support for potential applications of MSS as a functional food.

Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter.

Two Gram-stain-negative, aerobic, motile by means of flagella, short rod-shaped bacterial strains, designated IMCC43200T and IMCC45268T, were isolated from coastal seawater samples collected from the South Sea of Korea. Strains IMCC43200T and IMCC45268T shared 98.6% 16S rRNA gene sequence similarity and were closely related to Congregibacter litoralis KT71T (98.8% and 98.7%, respectively). Complete whole-genome sequences of IMCC43200T and IMCC45268T were 3.93 and 3.86 Mb in size with DNA G + C contents of 54.8% and 54.2%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 74.5% and 23.4%, respectively, revealing that they are independent species. The two strains showed ANI values of ≤ 75.8% and dDDH values of ≤ 23.0% to the type and only species of the genus Congregibacter (C. litoralis), indicating that each strain represents a novel species. Both strains contained summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and summed feature 8 (comprising C18:1 ω6c and/or C18:1 ω7c) as major fatty acid constituents. The predominant isoprenoid quinone detected in both strains was ubiquinone-8 (Q-8). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and aminolipids. Based on the phylogenetic, genomic, and phenotypic characterization, strains IMCC43200T and IMCC45268T were considered to represent two novel species within the genus Congregibacter, for which the names Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. are proposed with IMCC43200T (= KCTC 8133T = NBRC 116295T = CCTCC AB 2023139T) and IMCC45268T (= KCTC 92921T = NBRC 116135T) as the type strains, respectively.

Early and long-term responses of intestinal microbiota and metabolites to 131I treatment in differentiated thyroid cancer patients

BackgroundMultiple high doses of 131I therapy in patients with differentiated thyroid cancer (DTC) might disrupt the balance of gut microbiota and metabolites. This study aimed to investigate the alterations of intestinal bacteria and metabolism over two courses of 131I therapy, explore the interactions, and construct diagnostic models reflecting enteric microecology based on 131I therapy.MethodsA total of 81 patients were recruited for the first 131I therapy (131I-1st), among whom 16 received a second course (131I-2nd) after half a year. Fecal samples were collected 1 day before (Pre-131I-1st/2nd) and 3 days after (Post-131I-1st/2nd) 131I therapy for microbiome (16S rRNA gene sequencing) and metabolomic (LC–MS/MS) analyses.ResultsA total of six microbial genera and 11 fecal metabolites enriched in three pathways were identified to show significant differences between Pre-131I-1st and other groups throughout the two courses of 131I treatment. In the Post-131I-1st group, the beneficial bacteria Bifidobacterium, Lachnoclostridium, uncultured_bacterium_f_Lachnospiraceae, and Lachnospiraceae_UCG004 were abundant and the radiation-sensitive pathways of linoleic acid (LA), arachidonic acid, and tryptophan metabolism were inhibited compared with the Pre-131I-1st group. Compared with the Pre-131I-1st group, the Pre-131I-2nd group exhibited a reduced diversity of flora and differentially expressed metabolites, with a low abundance of beneficial bacteria and dysregulated radiation-sensitive pathways. However, less significant differences in microbiota and metabolites were found between the Pre/Post-131I-2nd groups compared with those between the Pre/Post-131I-1st groups. A complex co-occurrence was observed between 6 genera and 11 metabolites, with Lachnoclostridium, Lachnospiraceae_UCG004, Escherichia-Shigella, and LA-related metabolites contributing the most. Furthermore, combined diagnostic models of charactered bacteria and metabolites answered well in the early, long-term, and dose-dependent responses for 131I therapy.ConclusionsDifferent stages of 131I therapy exert various effects on gut microecology, which play an essential role in regulating radiotoxicity and predicting the therapeutic response.

First report of two Pantoea species causing bacterial leaf blight on wheat in the United States.

Wheat (Triticum aestivum) is an important crop worldwide, contributing to about one third of the global caloric intake. In June 2021, leaves with bacterial blight symptoms, including yellow and necrotic lesions running parallel to veins, were found in several fields across five counties in eastern Colorado (Weld, Morgan, Sedgwick, Baca, and Kit Carson). Plants exhibiting these symptoms were scattered throughout fields, but symptoms appeared consistent across counties. To determine the causal agent and complete Koch's postulates, a 1 cm2 symptomatic leaf area was excised and macerated in 0.5 mL of sterilized water from four field samples. The lysate was spread on yeast extract dextrose calcium carbonate medium (YDC agar, 1% yeast extract, 2% dextrose, 2% calcium carbonate, 1.5% agar) to isolate bacteria. Single colonies of yellow, mucoid morphology were selected and streaked on new YDC plates. Isolate genomic DNA was extracted (Zymo Research Quick-DNA Fungal/Bacterial Miniprep Kit, #D6005), and ~30 ng of gDNA was used to amplify the 16S rRNA, gyrB, and rpoB genes of all four isolates (Barret et al., 2015; Delétoile et al., 2009; Krawczyk et al., 2020; Ogier et al., 2019). Amplified PCR products were cleaned (Zymo DNA Clean & Concentrator kit, #D4033) and Sanger sequenced, and all sequences have been deposited in NCBI (16S rRNA: OR707336, OR707337, OR707338, OR707339), (gyrB: PP407951, PP407952, PP407953, PP407954), (rpoB: PP407955, PP407956, PP407957, PP407958). A BLAST search against whole genomes identified one isolate from Kit Carson county (CO314) and two isolates from Baca county (CO316 and CO317) as Pantoea agglomerans with 100% identity for the 16S rRNA, gyrB, and rpoB genes, and one isolate from Weld county (CO315) was 100% identical to Pantoea allii for all three genes. To complete Koch's postulates and confirm Pantoea sp. as the causal disease agents, isolates were grown as lawns on DifcoTM Nutrient Agar (NA) medium (48h, 28℃), suspended in 10 mM MgCl2 using a final optical density of 0.1 (~109 colony forming units per milliliter (CFU/mL)), and syringe-infiltrated into the entire leaf area of 10-day-old wheat seedling leaves (var. Hatcher). Treatments of 10mM MgCl2 and a field isolate that does not cause symptoms, identified as Pseudomonas synxantha by 16S rRNA and gyrB sequencing, were negative controls. Inoculated wheat plants were transferred to a growth chamber (22℃, 90% relative humidity). Symptoms developed 14 days post inoculation (dpi), with the most severe appearing 21 dpi. Each of the four Pantoea isolates were re-isolated from symptomatic leaves by grinding them in a Tissue Lyser II (Qiagen) with two metal beads and diluting with 0.4 mL of sterile water. A 20 µL sample of each isolate was plated on NA (24h, 28℃). The colonies appeared phenotypically identical to the original isolates, and Sanger sequencing confirmed the identities of the isolates. To our knowledge, this is the first report of P. agglomerans causing disease in wheat in the United States, and the first report of P. allii as a wheat disease-causing agent. This report is consistent with previous communications showing P. agglomerans causing wheat disease in China (Gao et al., 2023), and P. ananatis in Poland (Krawczyk et al., 2020). The growing numbers of reports of Pantoea spp. as pathogens in recent years suggests increasing novel disease emergence on cereals worldwide.

Molecular identification and morphological variations of Amblyomma lepidum imported to Egypt, with notes about its potential distribution under climate change.

The tick Amblyomma lepidum is an ectoparasite of veterinary importance due to its role in transmitting livestock diseases in Africa, including heartwater. This study was conducted in 2023 to monitor Amblyomma spp. infestation in dromedary camels imported from Somalia, Ethiopia, and Sudan to Egypt. This study inspected 200 camels at the Giza governorate's camel market that had been imported from Somalia, 200 from Ethiopia, and 200 from Sudan for tick infestation. Specimens were identified using morphological characteristics and phylogenetic analyses of the 12S and 16S rRNA genes. Clusters were calculated using an unweighted pair-group method with arithmetic averages (UPGMA) dendrogram to group the specimens according to their morphometric characteristics. The morphometric analysis compared the body shape of ticks collected from different countries by analyzing dorsal features. Principal component analysis (PCA) and canonical variate analysis (CVA) were performed to obtain body shape variation among specimens from different countries. Results indicated that camels were infested by 57 males Amblyomma lepidum, and no female specimens were observed; among these specimens, one may have a morphological abnormality. The results suggest that A. lepidum specimens collected from camels imported to Egypt from African countries exhibit locally adapted morphology with variations among specimens, particularly variations in body size. This adaptation suggests minimal potential for genetic divergence. Ecological niche modeling was used to predict the areas in Africa with suitable climates for A. lepidum. The study confirmed that East African countries might have the most favorable climatic conditions for A. lepidum to thrive. Interestingly, the amount of rain during the wettest quarter (Bio16) had the strongest influence on the tick's potential distribution, with suitability decreasing sharply as rainfall increased. Future predictions indicate that the climatic habitat suitability for A. lepidum will decrease under changing climate conditions. However, historical, current, and future predictions indicate no suitable climatic habitats for A. lepidum in Egypt. These findings demand continuous surveillance of A. lepidum in camel populations and the development of targeted strategies to manage tick infestations and prevent the spread of heartwater disease.

A new species of planthopper in the genus Colpoptera (Hemiptera:Fulgoroidea: Nogodinidae) from the Caribbean coast of Costa Rica

A new species of Colpoptera, C. stonei sp. nov., (Colpopterinae: Colpopterini) is described from Costa Rica, during a survey of planthoppers associated with palms. Molecular data for the five-prime region of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene, and 28S rRNA gene are provided for available members of Colpopterini to support placement in Colpoptera.

Genetic characterization of Cryptosporidium spp. in the North African hedgehog (Atelerix algirus) in the Canary Islands, Spain.

The North African hedgehog (Atelerix algirus) is an introduced species from Northwest Africa and is currently distributed in the Canary Islands. This species of hedgehog has been studied as a reservoir of enteropathogens, including Cryptosporidium spp. However, there are no data at species level. Therefore, the aim of the present study was to identify the Cryptosporidium species present in a population of hedgehogs (n = 36) in the Canary Islands. Molecular screening was performed using conventional polymerase chain reaction (PCR) targeting the small subunit ribosomal RNA (18S rRNA) gene of Cryptosporidium spp. Seven of the 36 fecal samples (19.45%) were positive and confirmed by nested PCR targeting the 18S rRNA gene and Sanger sequencing. Cryptosporidium parvum and Cryptosporidium muris were identified in 11.1% (4/36) and 5.6% (2/36) of the samples, respectively, while one sample could only be identified at the genus level. The zoonotic subtypes IIdA15G1 (n = 1), IIdA16G1b (n = 1), and IIdA22G1 (n = 1) of C. parvum were identified by nested PCR followed by analysis of the 60kDa glycoprotein (gp60) gene sequence. This study is the first genetic characterization of Cryptosporidium spp. in A. algirus, identifying zoonotic species and subtypes of the parasite.

Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios

Seasonal floodplains in the Amazon basin are important sources of methane (CH4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH4 fluxes. CH4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH4 oxidation pathways in mitigating CH4 emissions in Amazonian floodplains.

Sodium houttuyfonate Modulates the Lung Th1/Th2 Balance and Gut Microbiota to Protect Against Pathological Changes in Lung of Ovalbumin-induced Asthmatic mice.

The gut-lung axis involves microbial and product interactions between the lung and intestine. Antibiotics for chronic asthma can cause intestinal dysbiosis, disrupting this axis. Sodium houttuyfonate (SH) has diverse biological activities, including modifying gut microbiota, antibacterial, and anti-inflammatory. This study aims to explore the relationship between SH, CD4+ T cells, and gut microbiota. Allergic asthma was experimentally induced in mice through injection and inhalation of ovalbumin. After the administration of different amounts of SH, ELISA was utilized to ascertain the levels of inflammatory cytokines in the serum, flow cytometry was used to examine the levels of Th1/Th2 cytokines in CD4+ cells from lung tissues. The expression of T-bet and GATA3 in lung tissue was determined by Western blotting and quantitative real-time PCR assay. Gut microbiota was determined by 16S rRNA gene sequencing. The results showed that SH can alleviate pulmonary injury in asthmatic mice, reducing serum levels of IL-4, IL-5, and IL-13 while simultaneously increasing IFN-γ. Furthermore, SH has been observed to modulate the balance of Th1/Th2 cells by up-regulating the mRNA and protein expression of T-bet but down-regulating GATA3 in the lung tissues of asthmatic mice, thereby promoting the differentiation of Th1 cells. Additionally, SH can regulate the variety and composition of gut microbiota especially genus Akkermansia in asthmatic mice. SH can alleviate asthma through the regulation of Th1/Th2 cells and gut microbiota.

Kiwifruit-Agaricus blazei intercropping effectively improved yield productivity, nutrient uptake, and rhizospheric bacterial community

Intercropping systems have garnered attention as a sustainable agricultural approach for efficient land use, increased ecological diversity in farmland, and enhanced crop yields. This study examined the effect of intercropping on the kiwifruit rhizosphere to gain a deeper understanding of the relationships between cover plants and kiwifruit in this sustainable agricultural system. Soil physicochemical properties and bacterial communities were analyzed using the Kiwifruit-Agaricus blazei intercropping System. Moreover, a combined analysis of 16S rRNA gene sequencing and metabolomic sequencing was used to identify differential microbes and metabolites in the rhizosphere. Intercropping led to an increase in soil physicochemical and enzyme activity, as well as re-shaping the bacterial community and increasing microbial diversity. Proteobacteria, Bacteroidota, Myxococcota, and Patescibacteria were the most abundant and diverse phyla in the intercropping system. Expression analysis further revealed that the bacterial genera BIrii41, Acidibacter, and Altererythrobacter were significantly upregulated in the intercropping system. Moreover, 358 differential metabolites (DMs) were identified between the monocropping and intercropping cultivation patterns, with fatty acyls, carboxylic acids and derivatives, and organooxygen compounds being significantly upregulated in the intercropping system. The KEGG metabolic pathways further revealed considerable enrichment of DMs in ABC transporters, histidine metabolism, and pyrimidine metabolism. This study identified a significant correlation between 95 bacterial genera and 79 soil metabolites, and an interactive network was constructed to explore the relationships between these differential microbes and metabolites in the rhizosphere. This study demonstrated that Kiwifruit-Agaricus blazei intercropping can be an effective, labor-saving, economic, and sustainable practice for reshaping bacterial communities and promoting the accumulation and metabolism of beneficial microorganisms in the rhizosphere.

E-Cigarette Use, Cigarette Smoking, and Sex are Associated with Nasal Microbiome Dysbiosis.

Previous research suggests that e-cigarettes can alter immune function, including in the nasal mucosa, in unique ways. The respiratory microbiome plays a key role in respiratory host defense, but the effects of e-cigarettes on the respiratory or nasal microbiome, are not well understood. Using 16S rRNA gene sequencing on nasal samples from adult e-cigarette users, smokers, and nonsmokers, we determined that e-cigarette use and cigarette smoking are associated with differential respiratory microbiome dysbiosis and substantial sex-dependent differences in the nasal microbiome, particularly in e-cigarette users. Staphylococcus aureus, a common respiratory pathogen, was more abundant in both e-cigarette users and smokers in comparison with nonsmokers, while Lactobacillus iners, often consider a protective species, was more abundant in smokers but less abundant in e-cigarette users in comparison with nonsmokers. In addition, we identified significant dysbiosis of the nasal microbiome between e-cigarette users and smokers with high versus low serum cotinine levels, an indicator of tobacco product use and toxicant exposure. We also analyzed nasal lavage fluid for immune mediators associated with host-microbiota interactions. Our analysis identified disruption of immune mediators in the nose of e-cigarette users and smokers, which is indicative of disrupted respiratory mucosal immune responses. Taken together, our data identified unique, sex-dependent host immune dysfunction associated with e-cigarette use in the nasal mucosa. More broadly, our data highlight the need for continued inclusion and careful consideration of sex as an important variable in the context of toxicant exposures. This is the first study investigating the effects of e-cigarette use and sex on the nasal microbiome, which is considered an important gatekeeper for protecting the lower respiratory tract from pathogens. We found significant sex, exposure group, and serum cotinine level associated differences in the composition of the nasal microbiome, demonstrating the importance of considering sex in future nasal microbiome studies and warranting further investigation of the mechanisms by which e-cigarette use dysregulates nasal immune homeostasis.

Spatial Variation of Oomycetes and Bacteria on Surfaces, Solutions, and Plants from a Commercial Hydroponic Greenhouse

The spatial distribution and diversity of plant pathogens and other microbial communities in commercial operations is the first step in identifying critical control points where crops may be at risk of disease. Our objective was to characterize the spatial variation of oomycete pathogens and bacteria across the production system of a greenhouse producing lettuce in hydroponics. We utilized DNA metabarcoding to identify oomycetes and 16S rRNA gene sequencing of bacteria from different production stages and sample types (surfaces, solutions, and roots) collected from a commercial greenhouse producing lettuce in deepwater culture. Pythium was the genus with the highest relative abundance (41 to 100%) across all production stages. P. dissotocum was detected in most samples, except for sowing and seedling surfaces and municipal water, where P. myriotylum was the most abundant species. Oomycete communities showed distinct clustering by production stages and sample types, where sowing and seedling surfaces and municipal water were separated from the rest. Proteobacteria had the highest relative abundance in the surfaces at the sowing (98%) and seedling (85%) stages. Municipal water was the only sample with less than 20% relative abundance of Proteobacteria and dominated by Cyanobacteria. Negative correlations between Pythium and 13 bacteria genera point to potential antagonists in hydroponics that should be further studied. Mapping the spatial variation of oomycetes and bacterial communities in a commercial greenhouse indicates that production stage and sample type influence microbial composition and potentially the risk to disease.

Q2-metnet: QIIME2 package to analyze 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota.

16S rRNA gene sequencing is the most frequent approach for the characterization of the human gut microbiota. Despite different efforts in the literature, the inference of functional and metabolic interpretations from 16S rRNA gene sequencing data is still a challenging task. High-quality metabolic reconstructions of the human gut microbiota, such as AGORA and AGREDA, constitute a curated resource to improve functional inference from 16S rRNA data, but they are not typically integrated into standard bioinformatics tools. Here, we present q2-metnet, a QIIME2 plugin that enables the contextualization of 16S rRNA gene sequencing data into AGORA and AGREDA. In particular, based on relative abundances of taxa, q2-metnet determines normalized activity scores for the reactions and subsystems involved in the selected metabolic reconstruction. Using these scores, q2-metnet allows the user to conduct differential activity analysis for reactions and subsystems, as well as exploratory analysis using PCA and hierarchical clustering. We apply q2-metnet to a dataset from our group that involves 16S rRNA data from stool samples from lean, allergic to cow's milk, obese and celiac children, and the Belgian Flemish Gut Flora Project cohort, which includes faecal 16S rRNA data from obese and normal-weight adult individuals. In the first case, q2-metnet outperforms existing algorithms in separating different clinical conditions based on predicted pathway abundances and subsystem scores. In the second case, q2-metnet complements competing approaches in predicting functional alterations in the gut microbiota of obese individuals. Overall, q2-metnet constitutes a powerful bioinformatics tool to provide metabolic context to 16S rRNA data from the human gut microbiota. Python code of q2-metnet is available in https://github.com/PlanesLab/q2-metnet and https://figshare.com/articles/dataset/q2-metnet_package/26180446. Supplementary data are available at Bioinformatics online.

Clinical characteristics and logistic regression analysis of macrolide-resistant Mycoplasma pneumoniae pneumonia in children.

To investigate macrolide-resistant Mycobacterium pneumoniae (MRMP) pneumonia in children and construct a logistic regression model for mutations in the Mycoplasma pneumoniae drug-resistant gene. Clinical data of 281 children were analyzed. Sequencing confirmed a mutation at the A2063G locus of the 23S rRNA gene in 227 children (A2063G group); 54 children showed no mutations (non-MRMP [NMRMP] group). We compared clinical features, laboratory tests, imaging, and bronchoscopy results and constructed a multifactorial logistic regression model to analyze risk and protective factors. The A2063G group had longer durations of fever and hospitalization before admission, a higher proportion of treatment with sodium methylprednisolone succinate (MPS)/dexamethasone, longer time to discontinue hormones, and higher probability of combined infections. Monocyte percentage was significantly higher in the A2063G group. Imaging suggested a higher incidence of infections in the right lung compared to both lungs. Univariate analysis revealed fever duration before admission, hormone dose and duration, monocyte percentage, and mixed infections as risk factors for Mycoplasma pneumoniae infection with the A2063G mutation. The logistic regression model showed that mixed infections were an independent risk factor for the A2063G locus mutation, whereas hormone dose was a protective factor. A prevalence of macrolide resistance of 80.8% among children was observed in the region. Logistic regression analysis revealed that co-infection with other respiratory pathogens is an independent risk factor for the development of resistance genes, while the use of hormone dosage acts as a protective factor.

Functional diversity of bacterial microbiota associated with the toxigenic benthic dinoflagellate Prorocentrum.

Interactions between bacterial microbiota and epibenthic species of the dinoflagellate Prorocentrum may define the onset and persistence of benthic harmful algal blooms (bHABs). Chemical ecological interactions within the dinoflagellate phycosphere potentially involve a complex variety of organic molecules, metabolites, and toxins, including undefined bioactive compounds. In this study, the bacterial diversity and core members of the dinoflagellate-associated microbiota were defined from 11 strains of three epibenthic Prorocentrum species, representing three geographically disjunct locations within Mexican coastal waters. Microbiota profiles in stable monoclonal Prorocentrum cultures were obtained by sequencing amplicons of the V3-V4 region of the 16S rRNA gene. Thirteen classes of bacteria were identified among dinoflagellate clones, where Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia were consistently dominant. The bacterial community structure exhibited significantly different grouping by the location of origin of dinoflagellate clones. No significant diversity difference was found among free-living or unattached bacteria in the dinoflagellate culture medium (M) compared with those in closer association with the dinoflagellate host cells (H). Twelve taxa were defined as core members of the bacterial assemblage, representing the genera Algiphilus, Cohaesibacter, Labrenzia, Mameliella, Marinobacter, Marivita, Massilia, Muricauda, Roseitalea, and an unclassified member of the Rhodobacteraceae. The core members are inferred to significantly contribute to primary and secondary metabolic functions, but no direct correlation with dinoflagellate toxigenicity was apparent. Overall the bacterial profile and implied gene functionality indicated a suite of positive interactions, suggesting either mutualism or commensalism with the dinoflagellate. The further characterization and interpretation of specific gene functions and interactions between bacteria and dinoflagellates, such as epibenthic members of genus Prorocentrum, are key to understanding their role in toxigenesis and bHAB development.

Gut microbiome diversity within Clostridia is negatively associated with human obesity.

The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.

Metabolic versatility of anaerobic sludge towards platform chemical production from waste glycerol

Waste glycerol is produced in excess by several industries, such as during biodiesel production. In this work, the metabolic versatility of anaerobic sludge was explored towards waste glycerol valorization. By applying different environmental (methanogenic and sulfate-reducing) conditions, three distinct microbial cultures were obtained from the same inoculum (anaerobic granular sludge), with high microbial specialization, within three different phyla (Thermodesulfobacteriota, Euryarchaeota and Pseudomonadota). The cultures are capable of glycerol conversion through different pathways: (i) glycerol conversion to methane by a bacterium closely related to Solidesulfovibrio alcoholivorans (99.8% 16S rRNA gene identity), in syntrophic relationship with Methanofollis liminatans (98.8% identity), (ii) fermentation to propionate by Propionivibrio pelophilus strain asp66 (98.6% identity), with a propionate yield of 0.88 mmol mmol−1 (0.71 mg mg−1) and a propionate purity of 80–97% and (iii) acetate production coupled to sulfate reduction by Desulfolutivibrio sulfoxidireducens (98.3% identity). In conclusion, starting from the same inoculum, we could drive the metabolic and functional potential of the microbiota towards the formation of several valuable products that can be used in industrial applications or as energy carriers.Key pointsVersatility of anaerobic cultures was explored for waste glycerol valorizationDifferent environmental conditions lead to metabolic specializationBiocommodities such as propionate, acetate and methane were produced

Molecular identification of Halomonas AZ07 and its multifunctional enzymatic activities to degrade Pyropia yezoensis under high-temperature condition.

Pyropia yezoensis a commercially important red seaweed species, is susceptible to various microorganisms infections, among which bacterial infections are the most prominent ones. Pyropia yezoensis is often affected by harmful bacterial communities under high temperatures that can lead to its degradation and economic losses. The current study aimed to explore Pyropia yezoensis-associated microbiota and further identify potential isolates, which can degrade Pyropia yezoensis under high-temperature conditions. The 16S rRNA gene sequencing was used to identify the agarolytic bacterial species. The results showed that Chromohalobacter sp. strain AZ6, Pseudoalteromonas sp. strain AZ, Psychrobacter sp. strain AZ3, Vibrio sp. strain AZ, and Halomonas sp. strain AZ07 exhibited algicidal properties as these strains were more abundant at high temperature (25°C). Among the five isolated strains, the potential isolate Halomonas sp. strain AZ07 showed high production of agarolytic enzymes, including lipase, protease, cellulase, and amylase. This study confirmed that the isolated strain could produce these four different enzymes. The strain Halomonas AZ07 was co-treated with Pyropia yezoensis cells under two different temperature environments, including 13°C and 25°C. The degradation of Pyropia yezoensis occurred at the optimum temperature of 25°C and effectively degraded their cell wall, proteins, lipids, and carbohydrates. The successful cultivation of Pyropia yezoensis in coastal farm environments is dependent on specific temperature and environmental factors, and lower temperatures have been observed to be particularly beneficial for the survival and growth of Pyropia yezoensis. The temperature below 13°C was confirmed to be the best niche for the symbiotic relationship of microbiota associated with Pyropia yezoensis for its growth, development, and production.

A detailed analysis of 16S rRNA gene sequencing and conventional PCR-based testing for the diagnosis of bacterial pathogens and discovery of novel bacteria.

This study represents the first analysis of the bacterial community in chickens affected by swollen head syndrome, utilizing 16S rRNA gene sequencing. Samples were obtained from clinical laying chickens and were examined for the presence of Avibacterium paragallinarum (APG) and Ornithobacterium rhinotracheale (ORT) using conventional polymerase chain reaction (PCR). From the samples, five APG-positive (APG) and APG-negative (N-APG) samples were chosen, along with five specific pathogen-free chickens, for 16S rRNA gene sequencing. Results showed that APG and ORT were widely detected in the chicken samples with swollen head syndrome (SHS, 9/10), while APG was detected in all five specific pathogen-free (SPF) samples. In contrast, conventional PCR sensitivity was found to be inadequate for diagnosis, with only 35.7% (5/14) and 11.1% (1/9) sensitivity for APG and ORT, respectively, based on 16S rRNA gene sequencing data. Furthermore, 16S rRNA gene sequencing was able to quantify the bacteria in the samples, revealing that the relative abundance of APG in the APG group ranged from 2.7 to 81.3%, while the relative abundance of APG in the N-APG group ranged from 0.1 to 21.0%. Notably, a low level of APG was also detected in all 5 SPF samples. The study also identified a significant number of animal and human common bacterial pathogens, including but not limited to Gallibacterium anatis, Riemerella columbina, Enterococcus cecorum, Mycoplasma synoviae, Helicobacter hepaticus, and Staphylococcus lentus. In conclusion, 16S rRNA gene sequencing is a valuable tool for bacterial pathogen diagnosis and the discovery of novel bacterial pathogens, while conventional PCR is not reliable for diagnosis.

Uncovering the Antifungal Potential of Plant-Associated Cultivable Bacteria from the Aral Sea Region against Phytopathogenic Fungi

Two freshwater rivers, the Amu Darya and Syr Darya, flow into the Aral Sea, but they began to diminish in the early 1960s, and by the 1980s, the lake had nearly ceased to exist due to excessive water consumption for agriculture and the unsustainable management of water resources from rivers, which transformed the Aral Sea into a hypersaline lake. Despite this, the flora and fauna of the region began to evolve in the high-salinity seabed soil, which has received little attention in studies. In this study, we isolated approximately 1400 bacterial strains from the rhizosphere and phyllosphere of plant species of distinct families. Bacterial isolates were examined for antifungal activities against a range of pathogenic fungi such as Rhizoctonia gossypii, Trichothecium ovalisporum, Fusarium annulatum, F. oxysporum, F. culmorum, F. brachygibbosum, F. tricinctum, F. verticillioides, Alternaria alternata, A. terreus, Aspergillus niger, and As. flavus. Eighty-eight bacterial isolates exhibited varying antagonistic ability against pathogenic fungi. Furthermore, DNA barcoding of isolates using the 16S rRNA gene indicated that most antagonistic bacteria belonged to the Bacillus and Pseudomonas genera. The study also explored the activity of hydrolytic and cell-wall-degrading enzymes produced by antagonistic bacteria. The findings revealed that antagonistic bacteria can be utilized to widely protect seabed plants and plants growing in saline areas against pathogenic fungi, as well as agricultural crops.