High-throughput Sequencing Analysis Research Articles

Comparative Analysis of Gut Microbiota Composition in Yaks Across Different Geographical Region

Background: Despite the significance of gut microbiota in in determining the health and adaptability of the host, limited information exists regarding the influence of diverse geographic conditions on the intestinal microbiota of yaks. The study aimed at undertaking comprehensive comparison of microbiota composition in yaks originating from distinct geographic regions. Methods: 15 fecal samples were collected from yaks inhabiting 5 regions in China: Madoi, Nagqu and Deqin Shangri-la, Lhasa and Yushu. Through rigorous high-throughput sequencing analysis, the alpha diversity using metrics such as Shannon, ACE and Chao indices were assessed. Result: Notably, the Shangri-la samples exhibited the highest alpha diversity. Principal coordinate analysis revealed substantial variations in the composition of the intestinal microbiota across different regions. Firmicutes and Bacteroidetes emerged as the dominant phyla, with Ruminococcaceae being the most abundant family. Particularly, the genus Ruminococcaceae_UCG-005 demonstrated prominence, exhibiting higher abundance in Yushu samples compared to others. However, intriguingly, the predicted functional gene composition of the gut microbiota exhibited remarkable similarity across diverse geographical regions.

Effects of gradual increase of ciprofloxacin and cefotaxime on nitrogen and phosphorus removal and microbial community in moving bed biofilm reactor

To clarify the effects of trace amount of antibiotics in wastewater on biofilm reactor, this study explored the effects of gradual increase of ciprofloxacin (CIP) and cefotaxime (CTX) ranging from 100 to 1000 ng·L−1 on the nitrogen and phosphorus removal and microbial community in a moving bed biofilm reactor (MBBR). Under different phases of CIP and CTX gradual increase, the resilience of culturable functional bacteria including ammonifying bacteria, nitrite oxidizing bacteria, aerobic denitrifying bacteria and phosphorus accumulating organisms in the biofilm was analyzed. High-throughput sequencing analysis was used to reveal the microbial community structure and species composition of functional bacteria. The results indicated that the treatment performance of MBBR was temporarily affected by trace CIP and CTX and returned to its original level within 1–2 days. Under the condition of CIP and CTX concentration of 1000 ng·L−1, the COD, NH4+-N, TN and PO43−-P in the effluent were 49.68 mg·L−1, 0.18 mg·L−1, 7.82 mg·L−1 and 0.23 mg·L−1, respectively. Ammonifying bacteria exhibited strong resilience in trace CIP and CTX stress environments. Trace CIP and CTX altered the microbial community structure in biofilm, but the performance of nitrogen and phosphorus removal in MBBR was slightly affected. This might attribute to the rapid proliferation of Thauera, Dechloromonas and Candidatus_Accumulibacter on the carrier biofilm. The research results help to deepen the understanding of the impact of trace antibiotics on the MBBR and to provide a reference for the development of microbial germplasm resources for biological nitrogen and phosphorus removal from wastewater under antibiotic stress conditions.

Long Non-coding RNAs Influence Aging Process of Sciatic Nerves in SD Rats.

To investigate the long non-coding RNAs (lncRNAs) changes in the sciatic nerve (SN) in Sprague Dawley (SD) rats during aging. Eighteen healthy SD rats were selected at the age of 1 month (1M) and 24 months (24M) and SNs were collected. High-throughput transcriptome sequencing and bioinformatics analysis were performed. Protein-protein interaction (PPI) networks and competing endogenous RNA (ceRNA) networks were established according to differentially expressed genes (DEGs). As the length of lncRNAs increased, its proportion to the total number of lncRNAs decreased. A total of 4079 DElncRNAs were identified in Con vs. 24M. GO analysis was primarily clustered in nerve and lipid metabolism, extracellular matrix, and vascularization-related fields. There were 17 nodes in the PPI network of the target genes of up-regulating genes including Itgb2, Lox, Col11a1, Wnt5a, Kras, etc. Using quantitative RT-PCR, microarray sequencing accuracy was validated. There were 169 nodes constructing the PPI network of down-regulated target genes, mainly including Col1a1, Hmgcs1, Hmgcr. CeRNA interaction networks were constructed. Lipid metabolism, angiogenesis, and ECM fields might play an important role in the senescence process in SNs. Col3a1, Serpinh1, Hmgcr, and Fdps could be candidates for nerve aging research.

BCL6 confers resistance to HDAC inhibitors in DLBCL

Diffuse large B-cell lymphoma (DLBCL) is an aggressive non-Hodgkin lymphoma with limited response to chemotherapy. Histone acetylation is reduced in DLBCL. Chidamide, a histone deacetylase inhibitor, shows promise in lymphomas but needs further investigation for DLBCL. Our study indicated that chidamide effectively suppresses DLBCL both in vitro and in vivo. High-throughput RNA sequencing analysis provided comprehensive evidence that chidamide markedly influences crucial signaling pathways in DLBCL, including the MAPK, MYC and p53 pathway. Additionally, we observed substantial variability in the sensitivity of DLBCL cells to chidamide, and identified that elevated expression of BCL6 might confer resistance to chidamide in DLBCL. Moreover, our investigations revealed that BCL6 inhibited chidamide-induced histone acetylation by recruiting histone deacetylase (HDACs), leading to drug resistance in DLBCL cells. Furthermore, we found that lenalidomide targeted BCL6 degradation through the ubiquitination pathway and restore the sensitivity of drug-resistant DLBCL to chidamide. Collectively, these findings provided valuable insights into the global impact of chidamide on DLBCL and highlight the potential of targeting HDACs as a therapeutic strategy for DLBCL. Identifying BCL6 as a biomarker for predicting the response to chidamide and the combination therapy with BCL6 inhibition has the potential to lead to more personalized and effective treatments for DLBCL patients.

Microbial succession and flavor impact during natural fermentation of Tartary buckwheat sourdough

In this study, the succession process and driving mechanisms of microbial communities during the fermentation of Tartary buckwheat sourdough were explored using high-throughput sequencing and microbiome co-occurrence network analysis. A gas chromatograph–mass spectrometer (GC–MS) was used to monitor the dynamic evolution of flavor compounds in Tartary buckwheat sourdough at different fermentation stages. Using GC–MS and principal component analysis, 47 volatile compounds were identified as the main differential volatile compounds during fermentation. The predominant bacterial genera observed in the natural fermentation of Tartary buckwheat sourdough included Enterococcus, Weissella, Cronobacter, Lactococcus, and Pediococcus. Among fungi, Alternaria, Botrytis, Trichothecium, and Vishniacozyma were the dominant genera. The correlation analysis results revealed that Weissella, Pediococcus, Lactobacillus, Acinetobacter, and Vishniacozyma were the core functional microbes involved in flavor formation. Organic acids were the primary driving force for microbial succession. This study provides a better understanding of the relationship between microbial communities and volatile components in the natural fermentation process of Tartary buckwheat sourdough as well as useful information for improving the flavor quality of Tartary buckwheat sourdough products, thereby helping to choose starter cultures with flavor modulation ability.

The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals.

The Australian Biosecurity Genomic Database (ABGD) is a curated collection of reference viral genome sequences based on the Australian National Notifiable Disease List of Terrestrial Animals. It was created to facilitate the screening of high-throughput sequencing (HTS) data for the potential presence of viruses associated with notifiable disease. The database includes a single verified sequence (the exemplar species sequence, where relevant) for each of the 60 virus species across 21 viral families that are associated with or cause these notifiable diseases, as recognized by the World Organisation for Animal Health. The open-source ABGD on GitHub provides usage guidance documents and is intended to support building a culture in Australian HTS communities that promotes the use of quality-assured, standardized, and verified databases for Australia's national biosecurity interests. Future expansion of the database will include the addition of more strains or subtypes for highly variable viruses, viruses causing diseases of aquatic animals, and genomes of other types of pathogens associated with notifiable diseases, such as bacteria. Database URL: https://github.com/ausbiopathgenDB/AustralianBiosecurityGenomicDatabase.

Microbial Community Dynamics and Metabolite Changes during Wheat Starch Slurry Fermentation.

Wheat starch fermentation slurry is the main substrate for producing Ganmianpi, a traditional Chinese fermented wheat starch-based noodle. In the present work, the microbial population dynamics and metabolite changes in wheat starch fermentation slurry at different fermentation times (0, 1, 2, 3, and 4 days) were measured by using high-throughput sequencing analysis and headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME/GC-MS) methods. The texture and sensory properties of Ganmianpi made from fermented starch slurry are also evaluated. The results showed that Latilactobacillus curvatus and Leuconostoc citreum were the dominant bacteria in wheat starch fermentation slurry, while Saccharomyces cerevisiae and Kazachstania wufongensis were identified as the main species of fungi. With the extension of fermentation time, the reducing sugar content first increased and then decreased, when the titratable acidity content showed an increasing trend, and the nonvolatile acid was significantly higher than the volatile acid. A total of 62 volatile flavor compounds were identified, and the highest content is alcohols, followed by acids. Fermentation significantly reduced the hardness and chewiness of Ganmianpi, and increased its resilience and cohesiveness. Ganmianpi made from fermented starch slurry for two and three days showed a higher sensory score than other samples. The present study is expected to provide a theoretical basis for exploiting the strains with potential for commercial application as starter cultures and quality improvement of Ganmianpi.

Experimental research on biogenic methane generation pathway and microflora constraints based on in-situ gas-water-microbe

Biogenic coalbed methane (CBM), generated through the biodegradation process of coal organic matter, is a relatively clean and environment-friendly unconventional natural gas resource. To investigate the differences in microbial communities (bacteria and archaea) as well as their environmental influencing factors between the Permian Shanxi Formation (P1s) and Taiyuan Formation (P1t), we systematically collected in-situ CBM samples along with coalbed water and microbial samples from a representative biogenic CBM field – the Baode block locked in the Ordos basin in China. The relative content of biogenic CBM was quantitatively calculated while analyzing gas composition, stable isotope, ion content, and high-throughput sequencing analysis to discuss the generation pathway for biogenic CBM and environmental control factors affecting microbial community structure. The results indicate that P1s and P1t are mixed with early thermogenic gas and secondary biogenic gas genetic types within their respective CBMs. The average proportion for biogenic gas within current coal seams is approximately 62.24 % for P1s, while it reaches around 64.37 % for P1t. Water quality type primarily consists of Na-HCO3 type with total dissolved solids (TDS) measuring at approximately 1015.86 mg/L for P1s, whereas P1t exhibits Na-Ca-HCO3-Cl water type with TDS content reaching about 2314.85 mg/L. Combining dominant Methanobacterium species, along with Δ13C(CO2-CH4) ratios and δD(CH4) versus δD(H2O) indexes, represents the biogenic CBM primarily generated through the hydrogenotrophic methanogenesis pathway. The in-situ bacterial communities of P1s are mainly influenced by Ni, pH, and TDS. The archaeal communities exhibit higher sensitivity to environmental factors (such as Co, pH, Ni, and dissolved organic carbon) than bacteria. These findings hold significant implications for understanding the generation process of biogenic CBM in middle and low-rank coal areas.

Postinjury Pneumonia Induces a Unique Blood Microbiome Signature.

Previous preclinical studies have demonstrated a pathobiome after traumatic injury; however, the impact of post-injury sepsis on gut epithelial permeability and bacterial translocation remains unknown. We hypothesized that polytrauma with post-injury pneumonia would result in impaired gut permeability leading to specific blood microbiome arrays. Male and proestrus female Sprague-Dawley rats were subjected to either polytrauma (PT), PT plus 2-hours daily chronic restraint stress (PT/CS), PT with postinjury day 1 inoculation with pseudomonas pneumonia (PT + PNA), PT/CS + PNA, or naive controls. Whole blood microbiome was measured serially using high-throughput 16S rRNA sequencing and QIIME2 bioinformatics analyses. Microbial diversity was assessed using Chao1/Shannon indices and principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin and lipopolysaccharide-binding protein (LBP) assays. PT/CS + PNA had increased intestinal permeability compared to uninfected counterparts (PT/CS) with significantly elevated occludin (p < 0.01). Bacteria was not detected in the blood of naïve controls, PT or PT/CS, but was present in both PT + PNA and PT/CS + PNA on days two and seven. The PT/CS + PNA blood biome showed dominance of Streptococcus compared to PT + PNA at day two (p < 0.05). Females PT/CS + PNA had a significant abundance of Staphylococcus at day two and Streptococcus at day seven in the blood biome compared to male counterparts (p < 0.05). Multicompartmental trauma with post-injury pneumonia results in increased intestinal permeability and bacteremia with a unique blood biome, with sexual dimorphisms evident in the blood biome composition. These findings suggest that post-injury sepsis has clinical significance and could influence outcomes after severe trauma and critical illness.

Clinical Investigation of Bacteriome in Primary Endodontic Infections With Apical Periodontitis Using High-Throughput Sequencing Analysis

IntroductionThis study characterized the bacteriome in primary endodontic infection (PEI) with apical periodontitis (AP), identified core and rare bacteriome species and community diversity metrics, and analyzed the relationship between the bacteriome composition, diversity and features, and patient variables. MethodsTwenty-seven patients with PEI and AP were sampled. The DNA was extracted and quantified using quantitative polymerase chain reaction. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants, and taxonomic assignment of the amplicon sequence variants up to the species level was done against the Human Oral Microbiome Database. Core bacteriome and differential abundance analyses were performed using ANCOM. Alpha diversity was determined using Chao1, Shannon, and Simpson indexes. LeFse analysis was used to identify abundant taxa. Sparse Estimation of Correlations among Microbiomes analysis estimated linear and nonlinear relationships among bacteria. ResultsOf 27, 24 root canal samples were analyzed, and 3 root canal sampling were filtered out with a low read count. The bacterial phyla with top mean relative abundance were Bacteroidetes, Firmicutes, Synergistetes, Fusobacteria, and Actinobacteria. A total of 113 genera and 215 species were identified. The samples were gathered into 3 clusters. LefSe analysis identified differences in abundant taxa between distinct age, gender, symptomatology, and lesion size groups. Sparse Estimation of Correlations among Microbiomes distance analysis indicated Slackia exigua as the node with the highest degree. ConclusionsThe bacteriome in PEI with AP among the patients in this study was complex and displayed high microbial heterogeneity. Moreover, age, gender, symptomatology, and lesion size were associated with differences in bacteriome features in PEI with AP.

Exosomal circ-0100519 promotes breast cancer progression via inducing M2 macrophage polarisation by USP7/NRF2 axis.

Breast cancer (BC) is one of the most prevalent malignant tumours that threatens women health worldwide. It has been reported that circular RNAs (circRNAs) play an important role in regulating tumour progression and tumour microenvironment (TME) remodelling. Differentially expression characteristics and immune correlations of circRNAs in BC were verified using high-throughput sequencing and bioinformatic analysis. Exosomes were characterised by nanoparticle transmission electron microscopy and tracking analysis. The biological function of circ-0100519 in BC development was demonstrated both in vitro and in vivo. Western blotting, RNA pull-down, RNA immunoprecipitation, flow cytometry, and luciferase reporter were conducted to investigate the underlying mechanism. Circ-0100519 was significant abundant in BC tumour tissues and related to poor prognosis. It can be encapsulated into secreted exosomes, thereby promoting BC cell invasion and metastasis via inducing M2-like macrophages polarisation.Mechanistically, circ-0100519 acted as a scaffold to enhance the interaction between the deubiquitinating enzyme ubiquitin-specific protease 7 (USP7) and nuclear factor-like 2 (NRF2) in macrophages, inducing the USP7-mediated deubiquitination of NRF2. Additionally,HIF-1α could function as an upstream effector to enhance circ-0100519 transcription. Our study revealed that exosomal circ-0100519 is a potential biomarker for BC diagnosis and prognosis, and the HIF-1α inhibitor PX-478 may provide a therapeutic target for BC.

Identification of key genes involved in lignin and flavonoid accumulation during Tilia tuan seed maturation.

Transcriptomics and phenotypic data analysis identified 24 transcription factors (TFs) that play key roles in regulating the competitive accumulation of lignin and flavonoids. Tilia tuan Szyszyl. (T. tuan) is a timber tree species with important ecological and commercial value. However, its highly lignified pericarp results in a low seed germination rate and a long dormancy period. In addition, it is unknown whether there is an interaction between the biosynthesis of flavonoids and lignin as products of the phenylpropanoid pathway during seed development. To explore the molecular regulatory mechanism of lignin and flavonoid biosynthesis, T. tuan seeds were harvested at five stages (30, 60, 90, 120, and 150 days after pollination) for lignin and flavonoid analyses. The results showed that lignin accumulated rapidly in the early and middle stages (S1, S3, and S4), and rapid accumulation of flavonoids during the early and late stages (S1 and S5). High-throughput RNA sequencing analysis of developing seeds identified 50,553 transcripts, including 223 phenylpropanoid biosynthetic pathway genes involved in lignin accumulation grouped into 3 clusters, and 106 flavonoid biosynthetic pathway genes (FBPGs) grouped into 2 clusters. Subsequent WGCNA and time-ordered gene co-expression network (TO-GCN) analysis revealed that 24 TFs (e.g., TtARF2 and TtWRKY15) were involved in flavonoids and lignin biosynthesis regulation. The transcriptome data were validated by qRT-PCR to analyze the expression profiles of key enzyme-coding genes. This study revealed that there existed a competitive relationship between flavonoid and lignin biosynthesis pathway during the development of T. tuan seeds, that provide a foundation for the further exploration of molecular mechanisms underlying lignin and flavonoid accumulation in T. tuan seeds.

High-throughput sequencing analysis of differential microRNA expression in the process of blocking the progression of chronic atrophic gastritis to gastric cancer by Xianglian Huazhuo formula.

To explore the mechanism of Xianglian Huazhuo formula (, XLHZ) blocking the development of chronic atrophic gastritis (CAG) to gastric cancer (GC) through bioinformatics analysis and in vitro. Pathological morphology of gastric mucosa of rats were observed. High-throughput sequencing was used to analyze the miRNA expression profile of gastric mucosa. The miRanda, miRDB and miRWalk databases were used to predict the differential target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed for differential target genes. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differentially expressed miRNAs and target genes. Western blot, EdU, wound healing and flow cytometry were used to observe the effect of XLHZ on epithelial-mesenchymal transition (EMT) markers, proliferation, migration, apoptosis and cell cycle of CAG cells in vitro. A total of five differentially expressed miRNAs and four differential target genes were screened in this study. GO analysis showed that the target genes were enriched in regulation of neuron development, regulation of transcription factor activity and regulation of RNA polymerase. KEGG pathways database differences in gene enrichment of target genes in the Wnt signaling pathway, Phospholipase D signaling pathway and mitogen-activated protein kinase signaling pathway. qRT-PCR confirmed that miRNAs and its target genes were consistent with the screening results. In vitro, our study revealed that XLHZ could increase the expression of E-cadherin, decrease the expression of transforming growth factor β1, vimentin and β-catenin, inhibite the proliferation and migration of CAG cells, cause cell cycle arrest at G0/G1 and G2/M phase, induce the apoptosis of CAG cells, and prevent the progression of CAG to GC. This study provided a new idea for the mechanism of blocking the progression of CAG to GC by XLHZ, which may be related to the expression of miR-20a-3p, miR-320-3p, miR-34b-5p, miR-483-3p and miR-883-3p and their target genes transferrin receptor, nuclear receptor subfamily 4 member 2, delta like canonical Notch ligand 1 and a kinase anchor protein 12 in CAG. In the future, we will continue to investigate the linkage between the active ingredients of XLHZ and the relevant miRNAs and their target genes, so as to provide more sufficient experimental basis for clinically effective prevention of CAG to GC.

High-throughput single-molecule long-read RNA sequencing analysis of tissue-specific genes and isoforms in lettuce (Lactuca sativa L.)

Lettuce is one of the most widely cultivated and consumed dicotyledonous vegetables globally. Despite the availability of its reference genome sequence, lettuce gene annotation remains incomplete, impeding comprehensive research and the broad application of genomic resources. Long-read RNA isoform sequencing (Iso-Seq) offers substantial advantages for analyzing RNA alternative splicing and aiding gene annotation, yet it faces throughput limitations. We present the HIT-ISOseq method tailored for bulk sample analysis, significantly enhancing RNA sequencing throughput on the PacBio platform by concatenating cDNA. Here we show, HIT-ISOseq generates 3-4 cDNA molecules per CCS read in lettuce, yielding 15.7 million long reads per PacBio Sequel II SMRT Cell 8 M. We validate its effectiveness in analyzing six lettuce tissue samples, including roots, stems, and leaves, revealing tissue-specific gene expression patterns and RNA isoforms. Leveraging diverse tissue long-read RNA sequencing, we refine the transcript annotation of the lettuce reference genome, expanding its GO and KEGG annotation repertoire. Collectively, this study serves as a foundational reference for genome annotation and the analysis of multi-sample isoform expression, utilizing high-throughput long-read transcriptome sequencing.

Drought Stress Increases the Complexity of the Bacterial Network in the Rhizosphere and Endosphere of Rice (Oryza sativa L.)

The root microbiota plays a crucial role in assisting the plant host in combating various biotic and abiotic stresses, notably drought, which poses a significant threat to global food security. Despite extensive efforts to understand the shifts in rhizosphere and endosphere bacteriomes, there remains a gap in comprehending how drought stress influences the co-occurring network patterns within these compartments and their ecological functional potentials. To address this gap, a pot experiment was conducted with two treatments: continuous flooding as a control and drought treatment. Bulk soil, rhizosphere, and endosphere samples were collected and subjected to high-throughput sequencing and bioinformatics analysis. The results revealed that drought stress significantly reduced the rice biomass but increased the Shannon diversity index in both the rhizosphere and endosphere bacterial communities with no observable effect on richness across compartments. Additionally, drought treatment markedly altered the community structure and bacterial assemblages in these compartments, resulting in the specific enrichment of Actinobacteriota, Gemmatimonadetes, and Patescibacteria, while Bacteroidetes and Firmicutes were depleted in the rhizosphere and endosphere. Furthermore, drought heightened the complexity of the co-occurring networks and the proportions of positive links across all sampling compartments; this effect was accompanied by an increase in the number of connectors in the bulk soil and rhizosphere, as well as module hubs in the rhizosphere. Functional potential prediction indicated that drought stress significantly altered multiple potential ecological functions across all sampling compartments, particularly enriching functions related to the oxidation of sulfur, manganese, and hydrogen in the bulk soil, while functions associated with iron oxidation were significantly depleted in the rhizosphere. Overall, our results demonstrate that under drought stress, rice may specifically enrich certain bacterial taxa and enhance their positive interactions within its root system to improve adaptation.

Characteristics of microplastics and their abundance impacts on microbial structure and function in agricultural soils of remote areas in west China

As an emergent pollutant, microplastics (MPs) are becoming prevalent in the soil environment. However, the characteristics of MPs and the response of microbial communities to the abundance of MPs in agricultural soils in West China still need to be elucidated in detail. This study utilized the Agilent 8700 Laser Direct Infrared (LDIR) to analyze the characteristics of small-sized MPs (20–1000 μm) in soils from un-mulched and mulched agricultural fields in West China, and illustrated their correlation with microbial diversity. The results revealed a higher abundance of MPs in mulched soil ((4.12 ± 2.13) × 105 items kg−1) than that in un-mulched soil ((1.04 ± 0.26) × 105 items kg−1). The detected MPs were dominated by fragments, 20–50 μm and Polyamide (PA). High-throughput sequencing analysis indicated that alpha diversity (Chao1 and Shannon indices) in the plastisphere was lower compared to that in soil, and varied significantly with MPs abundance in soil. As the abundance of MPs increased, the proportion of soil about the degradation of organic matte and photoautotrophic taxa increased, which showed enrichment in the plastisphere. Functional predictions further indicated that MPs abundance affected potential soil functions, such as metabolic pathways associated with the C and N cycling. The plastisphere showed higher functional abundance associated with organic matter degradation, indicating higher potential health risks compared to soil environments. Based on the RDA analyses, it was determined that environmental physicochemical properties and MPs abundance had a greater impact on fungal communities than on bacterial communities. In general, the abundance of MPs affected the microbial diversity composition and potentially influenced the overall performance of soil ecosystems. This study offers empirical data on the abundance of MPs in long-term mulched agricultural fields and new insights for exploring the ecological risk issues associated with MPs.

A novel Saclayvirus Acinetobacter baumannii phage genomic analysis and effectiveness in preventing pneumonia

Acinetobacter baumannii, which is resistant to multiple drugs, is an opportunistic pathogen responsible for severe nosocomial infections. With no antibiotics available, phages have obtained clinical attention. However, since immunocompromised patients are often susceptible to infection, the appropriate timing of administration is particularly important. During this research, we obtained a lytic phage vB_AbaM_P1 that specifically targets A. baumannii. We then assessed its potential as a prophylactic treatment for lung infections caused by clinical strains. The virus experiences a period of inactivity lasting 30 min and produces approximately 788 particles during an outbreak. Transmission electron microscopy shows that vB_AbaM_P1 was similar to the Saclayvirus. Based on the analysis of high-throughput sequencing and bioinformatics, vB_AbaM_P1 consists of 107537 bases with a G + C content of 37.68%. It contains a total of 177 open reading frames and 14 tRNAs. No antibiotic genes were detected. In vivo experiments, using a cyclophosphamide-induced neutrophil deficiency model, tested the protective effect of phage on neutrophil-deficient rats by prophylactic application of phage. The use of phages resulted in a decrease in rat mortality caused by A. baumannii and a reduction in the bacterial burden in the lungs. Histologic examination of lung tissue revealed a decrease in the presence of immune cells. The presence of phage vB_AbaM_P1 had a notable impact on preventing A. baumannii infection, as evidenced by the decrease in oxidative stress in lung tissue and cytokine levels in serum. Our research offers more robust evidence for the early utilization of bacteriophages to mitigate A. baumannii infection.Key points•A novel Saclayvirus phage infecting A. baumannii was isolated from sewage.•The whole genome was determined, analyzed, and compared to other phages.•Assaying the effect of phage in preventing infection in neutrophil-deficient models.

Microbial Biodiversity of Cryoconites in Palandöken Mountain and Culturing Cold-Adapted Enzyme Producers

Palandöken Mountain is among the highest and coldest ecosystems of Türkiye, and knowledge on its microbial diversity has not been adequately characterized. The aim of the present study is to expand the current understanding of microbial diversity in Palandöken Mountain. Sampling studies were carried out at in winter an altitude of 2400–2900 m. A next-generation sequencing (NGS) based culture-independent approach was employed for elucidating the community structure in the 8 cryoconite samples using 16S and 23S rRNA gene sequencing. In addition, biotechnologically important cold-adapted enzyme producers were isolated and identified by employing conventional culture-dependent studies. High-throughput sequencing analysis revealed the presence of 36 bacterial and 2 fungal phyla. The bacterial communities of 8 samples were dominated by Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Acidobacteria. The fungal communities were dominated by Ascomycota and Basidiomycota. 2900 different taxonomic group for bacterial diversity and 51 for fungal diversity were reported in the present study. Furthermore, 25 cold-adapted enzyme-producers were isolated and identified in the culture-dependent studies. Each selected isolate was capable of producing at least one of the enzymes amylase, protease, lipase, cellulase and xylanase isolates were assigned to Aspergillus, Bacillus, Cladosporium, Dioszegia, Flavobacterium, Fusarium, Holtermanniella, Naganishia, Polaromonas, Protomyces, Pseudomonas Rhodosporidiobolus, Vishniacozyma and Yarrowia genera. Consequently, this is the first geomicrobiological investigation that describes bacterial and fungal diversity of cryoconites from Palandöken Mountain using an NGS-based culture-independent approach. Additionally, cultured cold-adapted enzyme producer isolates of the present study have a valuable potential for the development of new biotechnological tools for various industrial applications.

Interactions of graphene oxide with the microbial community of biologically active filters from a water treatment plant

With widespread occurrence and increasing concern of emerging contaminants (CECs) in source water, biologically active filters (BAF) have been gaining acceptance in water treatment. Both BAFs and graphene oxide (GO) have been shown to be effective in treating CECs. However, studies to date have not addressed interactions between GO and microbial communities in water treatment processes such as BAFs. Therefore, in the present study, we investigated the effect of GO on the properties and microbial growth rate in a BAF system. Synthesized GO was characterized with a number of tools, including scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDX), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and Raman spectrometry. GO exhibited the characteristic surface functional groups (i.e., C-OH, C=O, C-O-C, and COOH), crystalline structure, and sheet-like morphology. To address the potential toxicity of GO on the microbial community, reactive oxygen species (ROS) generation was measured using nitro blue tetrazolium (NBT) assay. Results revealed that during the exponential growth phase, ROS generation was not observed in the presence of GO compared to the control batch. In fact, the adenosine triphosphate (ATP) concentrations increased in the presence of GO (25 μg/L - 1000 μg/L) compared to the control without GO. The growth rate in systems with GO exceeded the control by 20 % to 46 %. SEM images showed that GO sheets can form an effective scaffold to promote bacterial adhesion, proliferation, and biofilm formation, demonstrating its biocompatibility. Next-generation sequencing (Illumina MiSeq) was used to characterize the BAF microbial community, and high-throughput sequencing analysis confirmed the greater richness and more diverse microbial communities compared to systems without GO. This study is the first to report the effect of GO on the microbial community of BAF from a water treatment plant, which provides new insights into the potential of utilizing a bio-optimized BAF for advanced and sustainable water treatment or reuse strategies.

Genetic analysis of yield components in buckwheat using high-throughput sequencing analysis and wild resource populations

Genetic analysis of yield components in buckwheat using high-throughput sequencing analysis and wild resource populations