16S rRNA Research Articles

Heavy metal exposure reduces larval gut microbiota diversity of the rice striped stem borer, Chilo suppressalis.

Cadmium (Cd), a widely distributed environmental pollutant in agroecosystems, causes negative effects on crops and herbivores through bottom-up processes. The gut microbial community of an insect can play a critical role in response to metal stress. To understand how microbiota affect the stress responses of organisms to heavy metals in agroecosystems, we initially used 16S rRNA sequencing to characterize the larval gut microbiota of Chilo suppressalis, an important agricultural pest, exposed to a diet containing Cd. The species richness, diversity, and composition of the gut microbial community was then analyzed. Results revealed that while the richness (Chao1 and ACE) of gut microbiota in larvae exposed to Cd was not significantly affected, diversity (Shannon and Simpson) was reduced due to changes in species distribution and relative abundance. Overall, the most abundant genus was Enterococcus, while the abundance of the genera Micrococcaceae and Faecalibaculum in the control significantly superior to that in Cd-exposed pests. Phylogenetic investigation of microbial communities by the reconstruction of unobserved states (PICRUSt) showed that the intestinal microorganisms appear to participate in 34 pathways, especially those used in environmental information processing and the metabolism of the organism. This study suggests that the gut microbiota of C. suppressalis are significantly impacted by Cd exposure and highlights the importance of the gut microbiome in host stress responses and negative effects of Cd pollution in agroecosystems.

Anthropogenic activities affect the diverse autotrophic communities of coastal sediments

Coastal sediments are a critical domain for carbon sequestration and are profoundly impacted by human activities. Therefore, it is essential to understand the structure and components of benthic autotrophs that play a crucial role in carbon sequestration processes, as well as the influence of anthropogenic activities on their communities. This study utilized an urban estuary, an industrial sea bay, a maricultural sea region, and two mangrove coastlines within the coastal areas of Guangdong Province, China. The micro-benthos in these environments, including prokaryotes and eukaryotes, were identified through high-throughput sequencing of 16S rRNA and 18S rRNA genes. The findings show that the autotrophic composition was altered by the interactions of anthropogenic heavy metals (Cd and Zn) and micro-eukaryotes (protazoa, metazoa, and parasitic organisms). Industrial pollution reduced the abundance of both prokaryotic and eukaryotic autotrophs. Mangroves induced a substantial transformation in the sediment eukaryotic and prokaryotic composition, increasing the proportion of autotrophs, notably sulfur-oxidizing and iron-oxidizing bacteria and microalgae. This alteration suggests an increase in specific sulfur and iron cycling with simultaneous carbon sequestration within mangrove sediments. These results indicate that anthropogenic activities affect sediment carbon sequestration by altering autotrophic assemblages along coastlines, thereby inducing consequential shifts in overall elemental cycling processes.

Association between salivary microbiota and tacrolimus pharmacokinetic variability in kidney transplant

Kidney transplantation (KT) serves as a highly effective treatment for end-stage renal disease (ESRD). Nonetheless, the administration of tacrolimus, a commonly used immunosuppressant in KT, faces challenges due to the lack of dependable biomarkers for its efficacy and the considerable variability in tacrolimus pharmacokinetics (TacIPV). In this study, 183 saliva samples from 48 KT recipients under tacrolimus therapy, alongside 9 healthy control samples, were subjected to 16S rRNA sequencing. The analysis revealed significant differences in the composition of salivary microbiota among KT recipients, patients with ESRD, and healthy controls. Moreover, trough blood concentrations (C0) of tacrolimus were associated with alterations in microbiota composition. Notably, Capnocytophage consistently exhibited a negative correlation in both group-level and individual trends. Furthermore, distinct taxa were identified that effectively distinguished recipients with varying TacIPV, as demonstrated by a cross-validation random forest model (mean AUC = 0.7560), with Anaerolinea emerging as a prominent contributor to the classifier. These findings suggest that salivary microbiota is closely linked to tacrolimus C0 levels and could aid clinicians in differentiating KT recipients based on TacIPV.

Study on Seroprevalence and Leptospiral Antibody Distribution Among Livestock Breeders and Farmers in Golestan Province.

The high prevalence of leptospirosis in humans is of great public health concern, particularly in tropical and subtropical regions. This study aimed to determine the seroprevalence of leptospiral antibodies and the distribution of serovars in livestock breeders and farmers in Golestan province. Seventy samples of serum collected from farmers and ranchers suspected of leptospirosis were examined using an ELISA method for surveying Immunoglobulin M (IgM) anti-leptospiria. Also from samples, DNA was extracted and PCR was performed using by primers for 16s rRNA. Demographic properties of positive patients were analysed. Chi-square statistical test shows a statistically significant difference between the gender and prevalence leptospirosis (p-value = 0.004). Also, by examining the age, it was shown that 68.57% of patients are in the middleaged rang. According to the results obtained from the study and investigation of blood serum IgM-and Immunoglobulin G (IgG) in people suspected of leptospirosis, 3 cases of the patients had IgM higher than 11 and were known to be positive for leptospirosis. Also, by examining the IgG level of patients, 5 cases had intermediate results, and 2 cases were found to be positive for IgG. The PCR results showed that 41.42% of patients tested positive for the 16s rRNA. Leptospirosis is a common disease among farmers, and in Golestan province, considering traditional farming methods, it is considered an important infectious disease. Therefore, health and safety measures should be expanded to control and prevent this disease. Also, by employing mechanised agricultural methods, the prevalence of leptospirosis in this region can be significantly reduced.

Gut microbiota and antibiotic resistance genes in endangered migratory Scaly-sided merganser (Mergus squamatus) in northeast China

Studying the diversity of gut microbiota and antibiotic resistance genes (ARGs) in endangered migratory birds, as well as their responses to different environments, can reflect the health status of migratory birds and the ecological risk of ARG transmission. The globally endangered Scaly-sided merganser (Mergus squamatus) is a typical migratory bird, yet the diversity of its intestinal microbiota and ARGs has not been reported. In this study, fecal samples were collected from two major riparian foraging areas utilized by M. squamatus in the Changbai Mountains of China: the Lushui River and the Manjiang River. The gut microbiota and ARG composition were characterized using 16S rRNA amplicon and metagenomic sequencing. The results indicated that the relative abundance of gut microbiota in the two habitats differed significantly, but the core flora was similar. Moreover, the relative abundance of pathogenic bacteria was high, suggesting that M. squamatus faces a high risk of disease. A total of 382 ARGs were identified, which were primarily resistant to multidrug, tetracycline, macrolides-lincosamides-streptogramins, and mupirocin. MsbA, abcA, rpoB2, and tetT were the most abundant shared ARGs between the two sites. The findings demonstrate that habitat influences the diversity of gut microbiota and ARGs in the endangered migratory M. squamatus. This species could serve as a reservoir for pathogenic bacteria and ARGs. Therefore, monitoring the diversity of gut microbiota and ARGs in M. squamatus across different habitats is essential for a comprehensive assessment of its health status and the ecological risk of ARG transmission in the future.

Microbiome and network analysis reveal potential mechanisms underlying Carassius auratus diseases: The interactions between critical environmental and microbial factors

Despite the rapid development of research on aquatic environment microbiota, limited attention has been paid to exploring the complex interactions between microbial communities and aquatic environments. Particularly, the mechanisms underlying fish diseases based on such dynamic interactions remain unknown. This study aimed to address the gap by conducting microbiome and co-occurrence network analyses on the typical freshwater aquaculture systems. High-throughput 16S rRNA gene sequencing results revealed significant differences in the microbiota between the disease and healthy groups. Notably, disease mortality varied consistently with the gradient of relative abundance of Proteobacteria (intestine, R2 = 0.46, p < 0.05) and Cyanobacteria (gill, R2 = 0.67, p < 0.01), indicating their potential use as diagnostic criteria. Furthermore, the elevated hepatosomatic index, NO3-N, COD and TC (sediment) were directly correlated with diseases (r > 0.54, p < 0.01). Mean concentrations of NO3-N, COD and TC were elevated by 78.87%, 25.63% and 44.2%, respectively, in ponds where diseases occurred. Quantitative analysis (qPCR) revealed that Aeromonas sobria infected hosts through a potential pathway of “sediment (4.4 × 105 copy number/g)-water (1.1 × 103 copy number/mL)-intestine (1.2 × 106 copy number/g)”. Similarly, the potential route for Aeromonas veronii was sediment (4.9 × 106 copy number/g) to gill (5.1 × 105 copy number/g). Additionally, the complexity of microbial networks in the intestine, water, and sediment was significantly lower in the disease group, although no similar phenomenon was observed in the gill microbial network. In summary, these findings reveal that elevated concentrations of crucial environmental factors disrupt the linkages within microbiota, fostering the growth of opportunistic bacteria capable of colonizing fish gut or gills. This offers new insights into potential mechanisms by which environmental factors cause disease in fish.

Mercury-tolerant metalophiles: A bio tool for remediation of mercury (Hg) affected Environs

Due to their low solubility, carcinogenic and mutagenic effects, heavy metals are of critical concern to humans and the environment. Mercury (Hg) is one of the rarest and least concentrated elements in the world, but it is ranked third in terms of toxicity. The present investigation evaluates the response and tolerance limit of bacteria isolated from the saffron soil of the Kashmir Valley to various mercury concentrations (50 ppm to 400 ppm). The minimum inhibitory concentration (MIC) was calculated after 24hours by measuring the optical density. Isolated bacteria have been characterized using two efficient methods, i.e. 16S rRNA gene sequence and MALDI-TOF MS. A total of 72 isolates were investigated for the mercury tolerance and among them, only 8 isolates (Staphylococcus equorum, Leclercia adecarboxylata, Staphylococcus warneri, Klebsiella pneumoniae, Serratia plymuthica, Bacillus megaterium, Pseudomonas putida and Bacillus safensis) were found tolerant to mercury with varying MIC. In comparison, Pseudomonas putida has been found to have the maximum resistance (400 ppm) for mercury and S. plymuthica and L. adecarboxylate had the lowest resistance level (200 ppm). The sequestration potential results revealed that P. putida executed the highest sequestration potential (73%) while K. pneumoniae showed the lowest sequestration potential (51.63%). Thus mercury tolerance capacity of these species may be utilised for detoxification and removal of mercury from polluted sites, providing an eco-friendly technique for bioremediation of mercury-affected environments.

Morphological and molecular identification of Eimeria rajasthani (coccidia: Eimeriidae) in the dromedary camel (Camelus dromedarius) in Riyadh, Saudi Arabia

IntroductionCoccidiosis is a serious parasitic disease in camels caused by an intestinal protozoan parasite of the genus Eimeria, which is linked to significant causes of reduced milk and meat production. In Saudi Arabia, scare literature focused on the coprological investigation of dromedary camels (Camelus dromedarius). To determine the taxonomic status of camel parasite species, we performed morphological characterization of oocysts and genetic analysis (18S rRNA and ITS-1 gene regions) of Eimeria species collected from camels in Riyadh, Saudi Arabia.MethodsA total of 150 faecal samples were obtained from camels at the old camel market. These samples were tested for the presence of Eimeria oocysts using the conventional floatation technique before being sporulated in a 2.5% potassium dichromate solution. Eimeria oocysts were morphologically and molecularly examined and identified, and the infection rate of parasitic infections was determined.ResultsOur findings revealed that the overall frequency of oocysts was 30%. The identified species was Eimeria rajasthani, which had a typical ellipsoidal oocyst shape. Oocystic polar granule, micropyle, micropylar cap, and oocyst residuum are not visible. Sporocysts are oval with stieda body. Sporocyst residuum contains many granules and sporozoites with refractile bodies and nuclei. Genetic analyses of the sequence data from the partial 18S rRNA and ITS-1 gene regions revealed that the sequences obtained from E. rajasthani oocysts are related to DNA sequences reported from E. lamae from the Alpaca from China, particularly the 18S rRNA sequences.ConclusionThis study emphasized the need to use molecular phylogenetic tools to describe camel intestinal coccidian parasites with traditional morphology-based approaches to better understand their biology. For camel husbandry and disease control, more studies should be conducted to better understand the epidemiology of these protozoan parasites.

DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea

The objective of this study was to evaluate the diversity and prevalence of tick-borne protists in the Republic of Korea via DNA barcoding using 18S rRNA gene fragments and PCR. Between 2021 and 2022, questing ticks were collected using the flagging method, with a total of 13,375 ticks collected and pooled into 1003 samples. Of these, 50 tick pools were selected for DNA barcoding targeting the V4 and V9 regions of 18S rRNA using the MiSeq platform. A taxonomic analysis of the amplicon sequence variants identified three genera of protozoa, namely Hepatozoon canis, Theileria luwenshuni, and Gregarine sp. However, the number and abundance of protists detected were different depending on the primer sets, and T. gondii was not identified in DNA barcoding. Furthermore, conventional PCR confirmed the presence of H. canis, Toxoplasma gondii, T. luwenshuni, and Theileria sp. in the collected ticks. This study identified H. canis and T. gondii in Ixodes nipponensis for the first time. It demonstrated that the results of DNA barcoding using 18S rRNA gene fragments can vary depending on the primer sets and further optimization is required for library construction to identify tick-borne protists in ticks. Despite these limitations, the findings highlight the potential of DNA barcoding using 18S rRNA gene fragments for screening the diversity of tick-borne protists in ticks.

Sustainable Abiotic-Biotic Dechlorination of Perchloroethene with Sulfidated Nanoscale Zero-Valent Iron as Electron Donor Source.

Combining organohalide-respiring bacteria with nanoscale zero-valent iron (nZVI) represents a promising approach for remediating chloroethene-contaminated aquifers. However, limited information is available regarding their synergistic dechlorinating ability for chloroethenes when nZVI is sulfidated (S-nZVI) under the organic electron donor-limited conditions typically found in deep aquifers. Herein, we developed a combined system utilizing a mixed culture containing Dehalococcoides (Dhc) and S-nZVI particles, which achieved sustainable dechlorination with repeated rounds of spiking with 110 μM perchloroethene (PCE). The relative abundance of Dhc considerably increased from 5.2 to 91.5% after five rounds of spiking with PCE, as evidenced by 16S rRNA gene amplicon sequencing. S-nZVI corrosion generated hydrogen as an electron donor for Dhc and other volatile fatty acid (VFA)-producing bacteria. Electron balance analysis indicated that 68.1% of electrons from Fe0 consumed in S-nZVI were involved in dechlorination, and 6.2, 1.1, and 3.2% were stored in formate, acetate, and other VFAs, respectively. The produced acetate possibly served as a carbon source for Dhc. Metagenomic analysis revealed that Desulfovibrio, Syntrophomonas, Clostridium, and Mesotoga were likely involved in VFA production. These findings provide valuable insights into the synergistic mechanisms of biotic and abiotic dechlorination, with important implications for sustainable remediation of electron donor-limited aquifers contaminated by chloroethenes.

Cover crop monocultures and mixtures enhance bacterial abundance and functionality in the maize root zone

Abstract Cover cropping is an effective method to protect agricultural soils from erosion, promote nutrient and moisture retention, encourage beneficial microbial activity, and maintain soil structure. Re-utilization of winter cover crop root channels by maize roots during summer allows the cash crop to extract resources from distal regions in the soil horizon. In this study, we investigated how cover cropping during winter followed by maize (Zea mays L.) during summer affects the spatiotemporal composition and function of the bacterial communities in the maize rhizosphere and surrounding soil samples using quantitative PCR, 16S rRNA gene amplicon sequencing, and metaproteomics. We found that the bacterial community differed significantly among cover crop species, soil depths, and maize growth stages. Bacterial abundance increased in reused root channels, and it continued to increase as cover crop diversity changed from monocultures to mixtures. Mixing Fabaceae with Brassicaceae or Poaceae enhanced the overall contributions of several steps of the bacterial carbon (C) and nitrogen (N) cycles, especially glycolysis and the pentose phosphate pathway. The deeper root channels of Fabaceae and Brassicaceae as compared to Poaceae corresponded to higher bacterial 16S rRNA gene copy numbers and improved community presence in the subsoil regimes, likely due to the increased availability of root exudates secreted by maize roots. In conclusion, root channel reuse improved the expression of metabolic pathways of the C and N cycles and the bacterial communities, which is beneficial to the soil and to the growing crops.

Multi-omics evaluation of clinical-grade human umbilical cord-derived mesenchymal stem cells in synergistic improvement of aging related disorders in a senescence-accelerated mouse model

BackgroundThe prevalence of age-related disorders, particularly in neurological and cardiovascular systems, is an increasing global health concern. Mesenchymal stem cell (MSC) therapy, particularly using human umbilical cord-derived MSCs (HUCMSCs), has shown promise in mitigating these disorders. This study investigates the effects of HUCMSCs on aging-related conditions in a senescence-accelerated mouse model (SAMP8), with a focus on DNA damage, gut microbiota alterations, and metabolic changes.MethodsSAMP8 mice were treated with clinical-grade HUCMSCs via intraperitoneal injections. Behavioral and physical assessments were conducted to evaluate cognitive and motor functions. The Single-Strand Break Mapping at Nucleotide Genome Level (SSiNGLe) method was employed to assess DNA single-strand breaks (SSBs) across the genome, with particular attention to exonic regions and transcription start sites. Gut microbiota composition was analyzed using 16S rRNA sequencing, and carboxyl metabolomic profiling was performed to identify changes in circulating metabolites.ResultsHUCMSC treatment significantly improved motor coordination and reduced anxiety in SAMP8 mice. SSiNGLe analysis revealed a notable reduction in DNA SSBs in MSC-treated mice, especially in critical genomic regions, suggesting that HUCMSCs may mitigate age-related DNA damage. The functional annotation of the DNA breaktome indicated a potential link between reduced DNA damage and altered metabolic pathways. Additionally, beneficial alterations in gut microbiota were observed, including an increase in short-chain fatty acid (SCFA)-producing bacteria, which correlated with improved metabolic profiles.ConclusionThe administration of HUCMSCs in SAMP8 mice not only reduces DNA damage but also induces favorable changes in gut microbiota and metabolism. The observed alterations in DNA break patterns, along with specific changes in microbiota and metabolic profiles, suggest that these could serve as potential biomarkers for evaluating the efficacy of HUCMSCs in treating age-related disorders. This highlights a promising avenue for the development of new therapeutic strategies that leverage these biomarkers, to enhance the effectiveness of HUCMSC-based treatments for aging-associated diseases.

Effects of fermented Arctium lappa L. root by Lactobacillus casei on hyperlipidemic mice

IntroductionThis study aimed to establish a fermentation system based on Lactobacillus casei (LC) and Arctium lappa L. root (AR) to investigate its effects. The objectives included comparing metabolite profiles pre- and post-fermentation using untargeted metabolomics and evaluating the impact of LC-AR in high-fat diet-induced hyperlipidemic mice.MethodsUntargeted metabolomics was used to analyze differences in metabolites before and after fermentation. In vitro antioxidant activity, liver injury, lipid levels, pro-inflammatory cytokine levels, and cholesterol-related mRNA expression were assessed. 16S rRNA sequencing was conducted to evaluate changes in gut microbiota composition.ResultsLC-AR exhibited stronger antioxidant activity and higher metabolite levels than AR. It also improved liver injury as well as better regulation of lipid levels, pro-inflammatory cytokine levels, and cholesterol-related mRNA. 16S rRNA analysis revealed that LC-AR decreased the Firmicutes/Bacteroidetes ratio, which correlated negatively with triglycerides, total cholesterol, and low-density lipoprotein cholesterol levels.DiscussionThese findings suggest that LC-AR may serve as a promising functional food and drug raw material for improving hyperlipidemia, particularly through its beneficial effects on gut microbiota and lipid regulation.

Dietary Administration Effects of Microbial Exopolysaccharide from Bacillus subtilis P1 on Growth Performance and Immunity in Nile Tilapia (Oreochromis niloticus)

Exopolysaccharide (EPS)-producing bacteria were isolated from the intestines of freshwater fish as prebiotics. Among the isolates, Bacillus sp. P1 was the potent EPS producer, with a high EPS production, and was then identified as Bacillus subtilis P1 based on 16S rRNA and biochemical characteristics. The produced microbial EPS was characterized by its functional groups by FTIR, showing a 90.20% correlation to inulin, while the EPS molecular weight was approximately 105 Da with a high PDI (&gt;1.5). Moreover, the EPS from B. subtilis P1 was assessed for prebiotic properties by growing probiotic bacteria, and significant cell growth occurred in sugar-free TSB with 0.5% EPS (p &lt; 0.05). EPS exhibited approximately 55.37% DPPH radical scavenging at 20 mg/mL and inhibited certain fish pathogens at 400 μg/mL (10–13 mm inhibition zone). Low EPS cytotoxicity was confirmed (&lt;1% hemolysis) prior to use as immunobiotics in Nile Tilapia (Oreochromis niloticus) diet supplementation. Nile tilapia growth and immune response were monitored after feeding with control (C), basal diet (BD), and treatment (T): BD + EPS 5 g/kg. In the T-group, the weight gain (WG), % specific growth rate (SGR), and average daily gain (ADG) significantly increased compared to the control (p &lt; 0.05) by week 4, with no negative effects on blood chemistry parameters. Lysozyme activity and respiratory burst activity in T-groups were significantly higher than the control (p &lt; 0.05), with a 50% RLP survival rate of Nile Tilapia infected by Aeromonas veronii in the T-group after a two-week challenge. On the other hand, the proximate analysis revealed higher protein content in the T-group. These findings suggest that EPS from B. subtilis P1 in fish diets efficiently supports fish growth and stimulates innate immune response in Nile Tilapia, thus showing potential as the immunobiotics for aquaculture.

Characterization of Sulfur Oxidizing Bacteria and Their Effect on Growth Promotion of Brassica napus L.

Oil seeds sector is one of the major dynamic components of the agriculture world. Oil seeds such as canola (Brassica napus) require a higher quantity of sulfur (S), which is supplied through inorganic fertilizers. However, the overapplication of agro-chemicals to get higher yields of crops is harming the soil health. Therefore, the application of bacterial cultures with plant growth-promoting activity as biofertilizers ensures soil health maintenance and enhances crop productivity. To achieve this aim, the present research was initiated by procuring three sulfur-oxidizing bacteria (SOBs), namely, SOB 5, SOB 10, and SOB 38, from the Microbiology Department, PAU. In the initial assessment, all three SOB cultures showed resilience to pesticide toxicity at the recommended dosage, with the exception of ridomil. These cultures were later characterized morphologically, biochemically, and at the molecular level using 16s rRNA resulting in their identification as Enterobacter ludwigii strain Remi_9 (SOB 5), Enterobacter hormaechei strain AUH-ENM30 (SOB 10), and Bacillus sp. 5BM21Y12 (SOB 38). Functional characterization of these SOB cultures revealed their ability to exhibit multifarious plant growth-promoting traits. Bacillus sp. 5BM21Y12 showed greater functional activity, including high P solubilization (14.903 µg/mL), IAA production (44.28 µg/mL), siderophore production (13.89 µg/mL), sulfate ion production (0.127 mM), ammonia excretion (2.369 µg/mL), and Zn solubilization (22.62 mm). Based on the results of functional and molecular characterization, Bacillus sp. 5BM21Y12 was selected for field trials by formulating different treatments. Composite treatment, T8 (100% S + Bacillus sp. + pesticides) significantly enhanced growth parameters (plant height, root, and shoot biomass), yield attributes (siliqua length, test weight, number of siliqua/plant), yield parameter (total biomass and seed yield), quality parameter (crude protein and oil) as compared to all other sole treatments employed in the field. A combined application of non-pathogenic Bacillus sp. 5BM21Y12, with good functional activity enhanced yield of crop due to synergistic and additive interaction with fertilizer/pesticides. As biofertilizer application reduces the input of pesticides/fertilizers new inoculant formulations with cell protectors and the development of compatible pesticides should be searched to assure the benefits of integrated treatment.

Comparative genomic analysis of two putative novel Idiomarina species from hypersaline miocene deposits

BackgroundHypersaline habitats, as extreme environments, are a great source of well-adapted organisms with unique properties as they have evolved various strategies to cope with these extreme conditions. Bioinformatics and genomic mining may shed light on evolutionary relationships among them. Therefore, the aim of this study was to assess the biodiversity and especially the strategies evolved within the Idiomarina genus, with the primary focus on the taxonomy and genomic adaptations of two novel strains affiliated with Idiomarina genus isolated from unique environment – brines of two Early Miocene salt deposits.ResultsBoth analyzed species belonged to the Idiomarina loihiensis cluster with similarity levels of 16S rRNA gene sequences as high as 99.5% and showed a significant genome size reduction, known characteristic of Idiomarina genomes, though within the genome of Sol25 strain the lowest extent of the carbohydrate utilization genes reduction was observed t among the Idiomarina species. Moreover, the comparative genome analyses indicated that despite both strains being isolated from geographically and geologically similar environments (brines from at least 12 Ma), the species showed higher relatedness to other Idiomarina species than to each other.ConclusionThe present findings highlighted the importance of genomic data in resolving taxonomic uncertainties and understanding of adaptation strategies of extremophiles. Geographic isolation likely contributed to population divergence of the Idiomarina genus, and the recent study offered insights into biogeographic patterns and allopatric speciation of this bacterial group.

Isolation of Heavy Metal-Tolerant and Anti-Phytopathogenic Plant Growth-Promoting Bacteria from Soils.

In this study, by isolating multifunctional soil bacteria that can promote plant development, resist heavy metals, exhibit anti-phytopathogenic action against plant diseases, and produce extracellular enzymes, we hope to improve the effectiveness of phytoremediation techniques. To isolate multifunctional soil bacteria, we used soils with diverse characteristics as isolation sources. To look into the diversity and structural traits of the bacterial communities, We conducted amplicon sequencing of the 16S rRNA gene on five types of soils and predicted functional genes using Tax4Fun2. The isolated bacteria were evaluated for their multifunctional capabilities, including heavy metal tolerance, plant growth promotion, anti-phytopathogenic activity, and extracellular enzyme activity. The genes related to plant growth promotion and anti-phytopathogenic activity were most abundant in forest and paddy soils. Burkholderia sp. FZ3 and FZ5 demonstrated excellent heavy metal resistance (≤ 1 mM Cd and ≤ 10 mM Zn), Pantoea sp. FC24 exhibited the highest protease activity (24.90 μmol tyrosine·g-DCW-1·h-1), and Enterobacter sp. PC20 showed superior plant growth promotion, especially in siderophore production. The multifunctional bacteria isolated using traditional methods included three strains (FC24, FZ3, and FZ5) from the forest and one strain (PC20) from paddy field soil. These results indicate that, for the isolation of beneficial soil microorganisms, utilizing target gene information obtained from isolation sources and subsequently exploring target microorganisms is a valuable strategy.

Co-frequency or contrary? The effects of Qiwei Baizhu Powder and its bioactive compounds on mucosa-associated microbiota of mice with antibiotic-associated diarrhea

Qiwei Baizhu Powder (QWBZP) has been proven effective in treating antibiotic-associated diarrhea (AAD), and the mechanism is associated with regulating the gut microbiota. However, the role of the bioactive compounds of QWBZP in regulating the gut microbiota is still unclear. In this study, 24 mice were divided into a normal control group (N), a model group (R), a QWBZP decoction group (TW), and a QWBZP-TG group (TG). AAD mouse models were established by mixed antibiotic administration. After modeling, mice in the TW group and TG group were treated with QWBZP decoction and QWBZP-TG, respectively. Mice in the N group and R group were gavaged with sterile water. 16S rRNA gene sequencing was used to investigate the changes of mucosa-associated microbiota (MAM) in the small intestine of mice. Moreover, the levels of diamine oxidase (DAO), D-Lactate, secretory immunoglobulin A (sIgA), interleukin 6 (IL-6), IL-10, and tumor necrosis factor-α (TNF-α) were detected using enzyme-linked immunosorbent assay (ELISA) kits. The results showed that QWBZP-TG significantly altered the diversity, structure, and abundance of MAM in the AAD mice. QWBZP-TG exerted a stronger suppression effect on Escherichia and Clostridium compared with QWBZP decoction. Meanwhile, QWBZP-TG downregulated the abundance of Lactobacillus, which elicited an opposite effect to QWBZP decoction. Prevotella was the signature bacteria that responded to the QWBZP-TG intervention. Furthermore, both QWBZP decoction and QWBZP-TG decreased the levels of DAO, D-Lactate, sIgA, IL-6, and TNF-α in the AAD mice. The role of glycosides is to help QWBZP ameliorate diarrhea symptoms by inhibiting the proliferation of diarrhea-associated bacteria, reducing inflammation and regulating immunity.

The intra-tumoral microbiome as a potential biomarker of response to external beam radiation therapy in cervical cancer

BackgroundWe aimed to determine the potential predictive value of the intra-tumoral microbiome as a marker of the response to external beam radiation therapy (EBRT) in cervical cancer (CC).MethodsA prospective longitudinal trial of 36 CC patients receiving pelvic radiotherapy was designed to investigate microbial characteristic signatures and diversity (alpha and beta) of multiple sites (tumor, vaginal, gut, urethral, and oral) in the superior response (SR) and inferior response (IR) groups of CC patients by 16S rRNA sequencing. Utilized the least absolute shrinkage and selection operator (LASSO) logistic regression method to analyze clinicopathological factors that potentially influenced the efficacy of EBRT. LEfSe analysis highlighted the microbiome features that best distinguished the categorized patient samples. Selected parameters were validated with Spearman correlation analysis, receiver operating characteristic (ROC) area under the curve (AUC) analysis and Kaplan-Meier survival analysis.ResultsFirstly, in our cohort, LASSO logistic regression analysis revealed no association between clinicopathological factors and EBRT efficacy. Subsequently, we employed 16S rRNA sequencing to compare microbiome differences across multiple sites and their correlations with major clinicopathological factors. We discovered that the intra-tumoral microbiome was independent of clinicopathologic features and represented the most direct and reliable reflection of the microbial differences between the SR and IR groups. We found lower alpha diversity in the tumor microbiome of SR group and identified the most relevant microbiome taxa (Bifidobacteriaceae, Beijerinckiaceae, and Orbaceae) associated with the efficacy of the response to EBRT in CC patients. We then conducted ROC analysis, finding that specific microbial taxa had an AUC of 0.831 (95% CI, 0.667–0.995), indicating the potential of these taxa as biomarkers for predicting EBRT efficacy. Kaplan-Meier survival analysis showed a better prognosis for patients with lower alpha diversity and higher relative abundance of Bifidobacteriaceae.ConclusionsOur data suggested that intra-tumoral specific microbiome taxa and lower alpha diversity may play an important role in the CC patient sensitivity to EBRT and offer novel potential biomarkers for predicting the response to EBRT efficacy.

Shen-Bai-Jie-Du decoction suppresses the progression of colorectal adenoma to carcinoma through regulating gut microbiota and short-chain fatty acids

BackgroundShen-Bai-Jie-Du decoction (SBJDD), a traditional Chinese herb formula developed based on evidence-based medicine, is efficacy to reduce the recurrence and carcinogenesis of colorectal adenoma. However, the mechanism of SBJDD to treat colorectal adenoma remains unclear. The present study aims to investigate the efficacy and mechanism of SBJDD on colorectal adenoma carcinogenesis from the aspects of regulating gut microbiota and short-chain fatty acids (SCFAs).MethodsTwenty-one patients diagnosed with colorectal adenoma were recruited in the study and required to take SBJDD for four consecutive weeks. Analysis of gut microbiota was conducted using 16S rRNA gene amplicon sequencing, while levels of SCFAs in fecal and serum samples were determined through HPLC–MS/MS. Additionally, twenty-four Apcmin/+ mice were randomly assigned to normal diet (ND), high-fat diet (HFD), and SBJDD groups. The pharmacological effects and mechanism of SBJDD on colorectal adenoma carcinogenesis were assessed using RT-qPCR, HE staining, IHC staining, Western blot, IF staining, and Flow cytometry assays.ResultsOur clinical study has shown that SBJDD can regulate the gut microbiota composition and enhance SCFAs production in patients with colorectal adenoma. SBJDD alleviated colorectal adenoma formation and carcinogenesis, as well as protected the integrity of the intestinal barrier in the Apcmin/+ mice model compared to the HFD group. Additionally, SBJDD was found to regulate gut microbiota capable of producing SCFAs. G protein-coupled receptors GPR43, GPR41, and GPR109a were effectively activated in the SBJDD group, while HDAC1 and HDAC3 were inhibited. Furthermore, decreased expression levels of interleukin 1 beta (IL-1β) and interleukin 6 (IL-6), along with elevated expression level of interleukin 10 (IL-10), were observed in the colorectal tissue of the SBJDD group. Finally, SBJDD exhibited the ability to reduce the proportion of M1-type macrophages while increasing the proportion of M2-type macrophages.ConclusionsOur study objectively demonstrated the pharmacological effects of SBJDD in inhibiting the progression of colorectal adenoma and investigated its mechanisms in terms of regulating gut microbiota, increasing SCFAs, and reducing colorectal inflammation.