Gene Research Articles

Phenotypic and genetic variation of Aedes albopictus (Diptera: Culicidae) in Thailand and its global relationships: Insights from wing morphometric and mitochondrial COI gene analyses.

Aedes albopictus (Diptera: Culicidae), commonly known as the Asian tiger mosquito, is an important vector transmitting dangerous arboviruses to humans. This study investigated the phenotypic and genetic variation of this species in Thailand through wing geometric morphometric (GM) and mitochondrial cytochrome c oxidase subunit I (COI) gene sequence analyses. A total of 236 Ae. albopictus specimens from 12 populations in Thailand and 89 specimens from invasive populations in Florida, Hawaii and Brazil underwent wing GM analysis. The centroid size (CS) of Ae. albopictus populations in Thailand ranged from 2.00 mm in Bangkok to 2.36 mm in Chanthaburi, while in invasive populations, CS varied from 2.25 mm in Brazil to 2.47 mm in Florida. Pairwise comparisons of wing shape revealed significant differences for most population pairs, with distances ranging from 1.63 to 10.02. The clustering tree indicated distant relationships in wing shape between native and invasive populations. Additionally, partial COI gene sequences were amplified from 108 specimens, revealing a mean haplotype diversity of 0.842 ± 0.025 and a mean nucleotide diversity of 0.002 ± 0.001. The results from neutral Tajima's D and Fu's Fs tests indicated negative and statistically significant values (-2.159 and -33.846, respectively), suggesting population expansion. Further examination of haplotype relationships between Thailand and other countries identified two distinct groups: a Southeast Asia group, with Thai haplotypes clustered exclusively within it, and a non-Southeast Asia group. These findings highlight the phenotypic and genetic variation of Ae. albopictus in Thailand, providing essential insights for disease control strategies and tracing the mosquito's origins across regions.

Development of a Nanobody-Alkaline Phosphatase Fusion Protein for Detection of SARS-CoV-2 Spike Protein in a Fluorescence Enzyme Immunoassay.

The continuous spread and evolution of severe acute respiratory symptom coronavirus 2 (SARS-CoV-2) necessitate the development of convenient and rapid detection methods. In this study, we developed a fluorescence enzyme immunoassay (FEIA) based on a nanobody (Nb)-alkaline phosphatase (ALP) fusion protein for detection of SARS-CoV-2 spike protein. The genetically modified anti-SARS-CoV-2 S-RBD Nb, Nb61, gene was fused with the ALP gene sequences via a flexible linker. Recombinant cloning was used to yield a recombinant prokaryotic expression plasmid, Nb61-ALP-His. The Nb61-ALP-His construct was transformed into E. coli BL21(DE3) and expressed in bacteria. Both Nb61 properties and ALP enzymatic activity were validated by colorimetric and fluorometric analysis. FEIA was optimized and established on the basis of the Nb61-ALP fusion protein. The detection limit of the FEIA was 3.18 ng/mL, with a linear range of 1.9-62.5 ng/mL. Comparison with a commercial kit indicated the reliability of the Nb61-ALP fusion-protein-based FEIA for monitoring the SARS-CoV-2 spike protein. This study highlights the potential of Nb-based enzyme immunoassays as a valuable tool for the rapid and accurate detection of SARS-CoV-2.

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.

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

Major QTL Mapping and Candidate Gene Analysis of Branching Number Habits in Cucumis melo

Branching number (BN) is a crucial architectural trait in Cucumis melo. Because of its multiple branch habits, much more labour costs are needed in melon production. However, the genetic mechanism of branching numbers in melon is not clear. Here, a genetic population from multiple branching material S8 (only two branching number in the first node) as the female line and S7 (multiple branching numbers in each node; more than nine branch numbers) as the male parent is used to make a cross F2:3 generation. By performing QTL mapping based on bulked segregate analysis (BSA) after two years, a candidate QTL region of the BN was located on chromosome 3. For further QTL mapping, a genetic linkage map, which contained 16 SSR markers with a total length of 2.27 Mb, was constructed. One major QTL locus bnDQ-2022-3.1 was detected between CmSSR9556 and CmSSR9580, with a LOD threshold of 11.37 and a contribution rate of 49.11% in the spring of 2022 in Daqing City. Then, a consistent QTL bnSY-2022-3.1 was also investigated in Sanya, Hainan Province, in the autumn of 2022, with a LOD threshold of 10.85 and a contribution rate of 45.01%. Nine genes were investigated within the interval of the candidate region located in chromosome 3 between 22,723,436 and 22,807,889 of the melon’s physical position within the 85.45 kb length region. Gene expression analysis showed significant differences between MELO3C019872.2.1, MELO3C030060.2.1, and MELO3C019871.2.1 in different development stages. Gene sequence different analysis revealed a “C”-to-“T” mutation in the 1280 bp site of MELO3C030060.2.1 in parental lines. Heterologous transformation of MELO3C030060.2.1 into cucumber revealed that overexpression of MELO3C030060.2.1 resulted in more and denser branches in cucumber plants, and the growth rate of lateral branches was significantly faster than that of the wild type. Transferring to antisense of MELO3C030060.2.1 had the opposite effect. To sum up, MELO3C030060.2.1 is related to melon branching initial habits. This study could provide a new insight into melon branching habits and provide a theoretical base for melon breeding.

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.

H and B Blood Antigens are Essential for In Vitro Replication of GII.2 Human Norovirus

Abstract Background Human norovirus (HuNoV) is a major cause of enteric infectious gastroenteritis and is classified into several genotypes based on its capsid protein amino acid sequence and nucleotide sequence of the polymerase gene. Among these, GII.4 is the major genotype worldwide. Epidemiological studies have highlighted the prevalence of GII.2. Although recent advances using human tissue- and induced pluripotent stem cell (iPSC)-derived intestinal epithelial cells (IECs) have enabled in vitro replication of multiple HuNoV genotypes can replicate, GII.2 HuNoV could only replicate in tissue-derived IECs, but not in iPSC-derived IECs. Methods We investigated the factors influencing GII.2 HuNoV replication in IECs, focusing on histo-blood group antigens. Additionally, we assessed the immunogenicity of GII.2 virus-like particles (VLPs) and their ability to induce neutralizing antibodies. Antibody cross-reactivity was tested to determine if GII.2 VLPs could neutralize other HuNoV genotypes, including GII.4, GII.3, GII.6, and GII.17. Results Our findings indicated that GII.2 HuNoV replication in vitro requires the presence of both H and B antigens. Moreover, GII.2 VLPs generated neutralizing antibodies effective against both GII.2 and GII.4 but not against GII.3, GII.6, or GII.17. Comparatively, GII.2 and GII.17 VLPs induced broader neutralizing responses than GII.4 VLPs. Conclusions This study suggests that GII.2 and GII.17 VLPs may be advantageous as HuNoV vaccine candidates because they elicit neutralizing antibodies against the predominant GII.4 genotype, which could be particularly beneficial for infants without prior HuNoV exposure. These insights will contribute to the development of effective HuNoV vaccines.

Identification of GiOMT gene family in Glycyrrhiza inflata bat and expression analysis under UV-B stresses

BackgroundO-Methyltransferase (OMTs) is a class of conserved multifunctional enzymes that play important roles in plant developmental regulation, hormone signaling, secondary metabolite synthesis and abiotic stress response. The GiOMT gene family has been identified and analyzed in species such as citrus, alfalfa, Populus and grape, but has not been reported in Glycyrrhiza inflata Bat.ResultsIn this study, we systematically identified and analyzed the GiOMT gene family of G. inflata by bioinformatics, and analyzed their physicochemical properties, conserved motifs, conserved structural domains, gene structures, phylogenetic relationships, chromosomal localization and fragment duplications, and the expression patterns of GiOMT genes in combination with transcriptomic data and qRT-PCR. The results showed that a total of 41 GiOMTs were identified in G. inflata, which were named GiOMT1 ~ GiOMT41 based on their chromosomal locations. Protein characterization showed that 29 GiOMT proteins were hydrophilic and 12 GiOMT proteins were hydrophobic. Subcellular predicted localization revealed that most GiOMT proteins localized in the cytoplasm and chloroplasts. Phylogenetic relationships showed that the OMT genes of three species, G. inflata, Arabidopsis and alfalfa, were distributed in three taxa, while the GiOMT genes were distributed in taxa I and II. Promoters of GiOMT genes contained light responsive element and many hormone responsive elements. The expression levels of GiOMT genes under UV-B stress were varied, indicating that GiOMT gene was in response to abiotic stresses in G. inflata.ConclusionIn this study, we investigated the genome-wide identification, structure, evolution and expression analysis of the GiOMT gene in G. inflata. The basal sequence of GiOMT genes was highly conserved throughout the evolutionary history of G. inflata. Most of the GiOMT genes were highly expressed in roots and were involved in the response to UV-B stress. The GiOMT genes may lead to the accumulation of flavonoids and enhancement of G. inflata quality and drug activity in G. inflata under UV-B radiation.

Comparative genome analysis of two peanut Ralstonia solanacearum strains with significant difference in pathogenicity reveals 16S rRNA dimethyltransferase RsmA involved in inducing immunity

BackgroundBacterial wilt disease, caused by Ralstonia solanacearum, seriously threaten the quality and yield of peanut (Arachis hypogaea L.). Identification of proteins inducing host immune response in R. solanacearum is an important way towards exploring resistance genes in peanut. In previous study, we found that the pathogenicity was significant different between peanut R. solanacearum ZKRS126 and ZKRS146. In this study, comparative genomics analysis was performed to reveal the difference of the genomes between ZKRS126 and ZKRS146, as well as the function of the strain specific gene rsmA in triggering immunity.ResultsCompared with ZKRS146, ZKRS126 caused less cell death in the peanut leaves and its proliferation and pathogenicity were significantly attenuated. Whole genome sequencing revealed that the genomes of ZKRS126 and ZKRS146 were composed of one chromosome, one megaplasmid and one small plasmid. The genome size of ZKRS126 (6,059,912 bp) was slightly larger than that of ZKRS146 (6,053,081 bp). Comparative genomics analysis showed that the genetic relationship between ZKRS126 and ZKRS146 was very close. In both ZKRS126 and ZKRS146, 73 Type III secretion system-secreted effectors (T3Es) were identified by retrieving the effector repertoire, respectively. The gene sequences of T3Es were identical between ZKRS126 and ZKRS146. Comparing all the coding genes between ZKRS126 and ZKRS146, 42 specific genes were identified in ZKRS126 and 43 in ZKRS146. Loss of the specific gene rsmA in ZKRS126 resulted in more virulence, and complementarity of rsmA in mutant strains recovered hypovirulence. The cAMP assay demonstrated RsmA was not a T3E. In Nicotiania benthamiana leaves, transient expression of rsmA significantly induced the up-regulated expression of marker genes in HR, PTI, SA, and JA pathways, indicating RsmA might trigger the plant immunity by activating the immune-related pathways.ConclusionsThis study not only obtained the complete genomes of two peanut R. solanacearum strains, but also revealed their differences in the genome levels through comparing analysis. The function verification of RsmA provided the way for the identification of immunity elicitors, which will accelerate the breeding of bacterial wilt-resistant peanut varieties in the future.Graphical

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.

Identification of a Novel FLT4 c.3028A>C Variant Associated With Milroy Disease.

VEGFR3 (FLT4) is crucial for embryonic lymphangiogenesis, and defects in this receptor can lead to congenital lymphedema type 1A (Milroy disease). This study analyses FLT4 gene sequence in 24 primary lymphedema patients, identifying genetic variants in five patients resembling typical Milroy disease. A novel likely pathogenic variant (c.3028A>C) was identified, and the pathogenicity of two previously described variants (c.3175G>C and c.3298T>C) was supported.

Antisense oligonucleotides as a targeted therapeutic approach in model of acute myeloid leukemia.

The genetic and epigenetic alterations observed in acute myeloid leukemia (AML) contribute to its heterogeneity, influencing disease progression response to therapy, and patient outcomes. The use of antisense oligonucleotides (ASOs) technology allows for the design of oligonucleotide inhibitors based on gene sequence information alone, enabling precise targeting of key molecular pathways or specific genes implicated in AML. Midostaurin, a FLT3 specific inhibitor and ASOs targeting particular genes, exons, or mutations was conducted using AML models. This ASOs treatment was designed to bind to exon 7 of the MBNL1 (muscleblind-like) gene. Another target was the FLT3 gene, focusing on two aspects: (a) FLT3-ITD (internal tandem duplication), to inhibit the expression of this aberrant gene form, and (b) the FLT3 in general. Treated and untreated cells were analyzed using quantitative PCR (qPCR), dot blot, and Raman spectroscopy. This study contrasts midostaurin with ASOs that inhibit FLT3 protein production or its isoforms via mRNA degradation. A trend of increased FLT3 expression was observed in midostaurin-treated cells, while ASO-treated cells showed decreased expression, though these changes were not statistically significant. In AML, exon 7 of MBNL1 is involved in several cellular processes and in this study, exon 7 of MBNL1 was targeted for method optimization, with the highest block of the exon 7 gene variant observed 48h post-transfection. Midostaurin, a multitargeted kinase inhibitor, acts against the receptor tyrosine kinase FLT3, a critical molecule in AML pathogenesis. While midostaurin blocks FLT3 signaling pathways, it paradoxically increases FLT3 expression.

Mathematical modeling of biohydrogen production via dark fermentation of fruit peel wastes by Clostridium butyricum NE95

BackgroundBiohydrogen production from agro-industrial wastes through dark fermentation offers several advantages including eco-friendliness, sustainability, and the simplicity of the process. This study aimed to produce biohydrogen from fruit and vegetable peel wastes (FVPWs) by anaerobic fermentative bacteria isolated from domestic wastewater. Kinetic analysis of the produced biohydrogen by five isolates on a glucose medium was analyzed using a modified Gompertz model (MGM). Besides, the feasibility of hydrogen production by Clostridium butyricum NE95 using FVPWs as substrates was investigated.ResultsThe bacterial isolate NE95 was selected as the highest biohydrogen producer with maximum biohydrogen production (Hmax) of 1617.67 ± 3.84 mL/L, Rmax (MGM) of 870.77 mL/L/h and lag phase (λ) of 28.37 h. NE95 was phenotypically and genetically identified as C. butyricum and its 16 S rRNA gene sequence was deposited in the GenBank under the accession number PP581833. The genetic screening of hydrogenase gene clusters indicated the presence of Fe-Fe hydrogenase gene in C. butyricum NE95. C. butyricum NE95 showed the ability to produce biohydrogen from different FVPWs, with watermelon and melon peels being the most promising feedstocks for fermentation. It was revealed that using a mixture (1:1, w/w) of watermelon and melon peels as a substrate for C. butyricum NE95 significantly increased biohydrogen yield with Hmax of 991.00 ± 10.54 mL/L, Rmax of 236.31 mL/L/h, λ of 33.92 h and a high accuracy of R2 (0.997).ConclusionsThe study highlights the effectiveness of C. butyricum NE95 on the valorization of FVPWs and generates a sustainable source of biohydrogen production.

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.

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).

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).

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.