16S RNA Research Articles

Phylogenetic Profile of Nonulcerans and Nontuberculous Environmental Mycobacteria Isolated in Côte d'Ivoire.

Environmental mycobacteria are involved in several infections ranging from lung to skin infections. In Côte d'Ivoire, apart from Mycobacterium ulcerans and Mycobacterium tuberculosis, little information exists on other species. The culture of these species, a real challenge, especially in developing countries like Cote d'Ivoire, limits their identification. However, there are reports in literature of infections caused by these mycobacteria, and few species have never been described in human or animal infections. These are difficult cases to treat because of their resistance to most antituberculosis antibiotics. The aim of our work was to study the diversity of potentially pathogenic mycobacterial species in wastewater drainage channels in different townships and in two hospital effluents in the city of Abidjan. Wastewater samples were cultured, followed by conventional polymerase chain reaction (PCR) targeting mycobacterial 16S ribonucleic acid (16S RNA) using PA/MSHA primers. 16 S RNA identified were sequenced by Sanger techniques. Sequences obtained were analyzed, and a phylogenic tree was built. Fast-growing mycobacteria, including Mycobacterium fortuitum, Mycobacterium phocaicum, Mycobacterium sp., and others presence, were confirmed both by culture and molecular techniques. M. fortuitum strain was the same in effluents of the Treichville University Hospital and in the wastewater of the township of Koumassi. New species never isolated in Côte d'Ivoire, such as M. phocaicum, have been identified in wastewater of the township of Yopougon. This study showed that the sewer network in the city of Abidjan is colonized by both potentially pathogenic mycobacteria and saprophytic environmental mycobacteria.

Biofloc biosecurity: A revolutionary paradigm in augmenting aquaculture health and resilience against Aeromonashydrophila

This research embarked upon an in-depth exploration of the pioneering concept of biofloc biosecurity, assessing its instrumental role in amplifying fish growth dynamics, hematological indices, biochemical metrics, chemical body composition, and immunological defenses, both pre- and post-infection by Aeromonas hydrophila. By juxtaposing biofloc-reared Oreochromis niloticus against traditionally reared fish, intricate observations of histopathological changes and clinical symptomatology were undertaken. Employing 16S RNA, the bacterial strain Aeromonas hydrophila (ATCC 7966) was precisely identified and banked It into gene bank and given accession number (OR452335). After a preparatory period of ten weeks in the Biofloc system, O. niloticus faced a challenge with Aeromonas hydrophila. Empirical findings revealed that fish from the Biofloc cohort displayed marked advancements across all investigational parameters, before and after infection, as opposed to the control set. In the aftermath of the Aeromonas hydrophila confrontation, biofloc-acclimatized fish manifested an elevated resilience against the bacterial onslaught, displaying superior metrics in growth, hematology, biochemistry, body constitution, and immunological response. Biofloc group showed a strong immune response, particularly in terms of Lysozyme and Total Antioxidant Capacity. Additionally, there was a significant impact on Immunoglobulin and Complement 3 after infection, highlighting the group's increased immune activity. Furthermore, these fish attenuated the pernicious morphological indicators and histopathological anomalies instigated by septicemic bacteria, which otherwise inflict substantial economic detriments upon the aquaculture industry. This research underscores the immense promise biofloc biosecurity holds in bolstering the overall health and performance metrics of cultured O. niloticus.

Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis.

Liver metastasis is a major cause of mortality in patients with advanced stages of colorectal cancer (CRC). The gut microbiota has been demonstrated to influence the progression of liver diseases, potentially providing novel perspectives for diagnosis, treatment and research. However, the gut microbial characteristics in CRC with liver metastasis (LM) and with no liver metastasis (NLM) have not yet been fully established. In the present study, high-throughput 16S RNA sequencing technology was employed, in order to examine the gut microbial richness and composition in patients with CRC with LM or NLM. A discovery cohort (cohort 2; LM=18; NLM=36) and a validation cohort (cohort 3; LM=13; NLM=41) were established using fresh feces. In addition, primary carcinoma tissue samples were also analyzed (LM=8 and NLM=10) as a supplementary discovery cohort (cohort 1). The findings of the present study indicated that the intestinal microbiota richness and diversity were increased in the LM group as compared to the NLM group. A significant difference was observed in species composition between the LM and NLM group. In the two discovery cohorts with two different samples, the dominant phyla were consistent, but varied at lower taxonomic levels. Phylum Fusobacteria presented consistent and significant enrichment in LM group in both discovery cohorts. Furthermore, with the application of a random forest model and receiver operator characteristic curve analysis, Fusobacteria was identified as a potential biomarker for LM. Moreover, Fusobacteria was also a poor prognosis factor for survival. Importantly, the findings were reconfirmed in the validation cohort. On the whole, the findings of the present study demonstrated that CRC with LM and NLM exhibit distinct gut microbiota characteristics. Fusobacteria detection thus has potential for use in predicting LM and a poor prognosis of patients with CRC.

Abstract 2176: Differences in gut microbial composition alter pancreatic tumorigenesis

Abstract Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second leading cause of cancer-related deaths by 2030, and currently has a 5-year survival rate of roughly 10%. With long-term survival rates in patients being exceedingly low, understanding what factors delineate survival is imperative. When comparing spontaneous transgenic mouse models of pancreatic cancer housed in geographically distinct vivaria, regardless of a common lineage, we observed drastically different phenotype states in the respective locations. We hypothesize that the gut microbiome results in different gene expression profiles, leading to alterations in pancreatic tumorigenesis. Using various sequencing techniques, including 16s rRNA and RNA sequencing of the gut, we identified unique signatures at these respective institutions. Subsequent fecal microbiota transplantation and single bacterial species colonization experiments were performed to evaluate the ability of microbiomes/specific microbiota to alter the rate of tumorigenesis. In addition to probing the gut microbiome, circulating metabolites from individual mice were quantified, and correlated to phenotype state. Following identification of potentially tumorigenic bacterially derived metabolites, single bacteria colonization experiments were utilized to determine the downstream effects of identified metabolites as well as the ability of directly altering the metabolic landscape to drive tumorigenesis. Additionally, murine derived pancreatic cancer cells were exposed to both identified bacteria alone or bacterially produced metabolite and analyzed by metrics such as proliferation and relative expression of transcription factors associated with cancer development in vitro. Taken together, these data demonstrate the ability of distinct gut microbiomes to directly alter the metabolic landscape in mice, thus differentially altering the progression of pancreatic lesions. By better understanding the factors that stratify survivorship, we can begin to employ clinically actionable methodologies in the treatment or prevention of pancreatic cancer. Citation Format: Rian M. Howell, Jose Enriquez Ortiz, Olivia Le Roux, Vidhi Chandra, Le Li, Pratip K. Bhattacharya, Florencia McAllister. Differences in gut microbial composition alter pancreatic tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2176.

Abstract 6689: Modulation of MAITs by the tumor microbiome in anti-PD1 treated cancers

Abstract Mucosal associated invariant T (MAIT) cells are innate like T-cells that recognize non-peptide metabolite antigens presented on monomorphic MHC related-1 (MR1) making them an attractive off the shelf tool for cancer immunotherapy. In this study, we investigate the function of MAITs in the tumor microenvironment of neoadjuvant anti-PD1 treated lung cancer patients (NCT02259621)). Paired single cell RNA/TCR sequencing analysis revealed an oligoclonal expansion of MAITs comprising of canonical TRAV1-2+ and non-canonical MAITs TRAV1-2-. TCR capture from canonical MAIT clonotypes confirmed their in vitro recognition of 5-OP-RU, bacteria derived riboflavin derivative as well as MR1 dependent recognition of live bacteria present in the tumor. However, the nature of antigens recognized by non-canonical MAITs remains poorly understood. On mining transcriptional profiles of MAITs, we observed that canonical MAITs were characterized by high clonal amplification whereas the non-canonical clonotypes expressed a strong activation/exhaustion gene signature. This suggests that both these MAIT populations recognize different types of antigens, differentially activate, and respond to immune checkpoint blockade (ICB), the non-canonical MAITs being highly dysfunctional. Using bacterial 16S RNA amplicon and metagenomics sequencing, we seek to identify microbial and metabolomics signatures associated with MAIT activation and response to ICB. We identified MAITs to express a cytotoxic signature making them a potential target for cancer immunotherapy. Our findings will provide further insights into the nature of ligands recognized by MAITs and the mechanisms associated with MR1 dependent recognition and tumor killing. Investigating the role of unconventional T-cells in response to ICB has the potential to reveal new tumor-associated antigens which could open avenues into innovative combination immunotherapies. Citation Format: Pakhi Birla, Lansaol Yang, Cynthia Sears, Fyza Shaikh, Drew Pardoll, Franck Housseau. Modulation of MAITs by the tumor microbiome in anti-PD1 treated cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6689.

Identification of suitable reference genes for RT-qPCR studies in human parathyroid tissue glandular cells

Identifying a proper reference gene allows us to understand fundamental changes in many biological processes. Normalization during gene expression analyses is essential for every tissue/cell type, including parathyroid tissue glandular cells. Quantitative method of gene expression analyses via qRT-PCR method provides the accurate examination of every target gene. There are limited reports to present commonly used reference genes in human parathyroid tissues rather than for glandular cell types. This study aims to determine and compare the most stable to least stable genes for parathyroid tissue cells. 43 human parathyroid tissue obtained from primary and secondary hyperparathyroidism patients and glandular cells isolated enzymatically by the removal of extracellular matrix components. After extraction of the total RNA, cDNA synthesis was performed, then qRT-PCR evaluated 14 candidate reference genes. Stability was determined by RefFinder software (Delta ct, BestKeeper, Genorm, and NormFinder algorithms), and the outcome was evaluated for five groups. Even if assessed with different groups, the most stable genes were RPLP0 and GAPDH, while the CLTC and RNA 18S were the least stable. We have confirmed the comprehensive ranking of the most stable three genes alone with the NormFinder algorithm to understand intergroup variation and found out that RPLP0>GAPDH>PGK1. Lastly, comparisons of relative target gene (GCM2) expression revealed similar expression patterns for the most stable reference genes. The most stable reference gene is recommended for the stages where stability is evaluated using the results of four different approaches using RefFinder. We aspire for this study to assist future research to conduct thorough assessments of appropriate reference genes before engaging in gene expression analyses for parathyroid tissue.

Evaluation of the protective bioactivity and molecular mechanism verification of lactoferrin in an Alzheimer's mouse model with ulcerative enteritis

The development of new drug therapies for Alzheimer's disease (AD) is an important research topic today, but the pathogenesis of AD has not been thoroughly studied, and there are still several shortcomings in existing drug therapies. Therefore, this study aimed to explore the molecular mechanism of lactoferrin (LF) in the treatments of AD and ulcerative colitis (UC) that is susceptible to AD, starting from the principle of one drug, two diseases, and the same treatment. This study used pathological staining and specific indicator staining to preliminarily evaluate the interventions of LF on UC injury and AD progression. We also used 16s RNA full-length sequencing to investigate the effect of LF on the abundance of intestinal microbiota in AD mice. Intestinal tissue and brain tissue metabolomics analysis were then used to screen specific metabolic pathways and preliminarily verify the metabolic mechanism of LF in alleviating the 2 diseases by regulating certain specific metabolites. Moreover, LF significantly changed the types and abundance of gut microbiota in AD mice complicated by UC. To conclude, this study proved the clinical phenomenon of AD susceptibility to UC, and verified the therapeutic effect of LF on 2 diseases. More importantly, we revealed the possible molecular mechanism of LF: Not only does it enrich the cognitive level of LF in alleviating AD by regulating the gut microbiota through the brain gut axis from the perspective of the theory of food nutrition promoting human health, but it also provides a practical basis for the subsequent research and development of LF and drug validation from the perspective of drug food homology.

Electrochemical behaviour of thermally treated aluminium 2024 alloy exposed to B. mojavensis

The copper-rich zone plays a key role in understanding the deterioration process of 2024 aluminium alloy. The intermetallic on the surfaces makes this alloy susceptible to both local corrosion and microbial colonization. The adhesion of bacteria on the surface could deteriorate the metallic substrate in a phenomenon known as microbiologically influenced corrosion (MIC). The triggering mechanism of MIC in 2024-T3 is unclear. An electro­chemical study was conducted to determine the influence of the second phase (Al2Cu) on the corrosion of the 2024-T3 aluminium alloy exposed to bacteria. The 2024-T3 alloy was thermally treated to increase the amount of Al2Cu by nearly 67 % on the surface. The bacterium under study was collected from the corrosion products of a Chilean Air Force aircraft. The isolated bacterium was identified by 16S RNA sequencing as Bacillus mojavensis (99.99 %). Results obtained by electrochemical impedance spectroscopy showed a decreased impedance of 2024-T3 and an increased impedance of heat-treated, both samples exposed to bacteria. The increased impedance could be associated with the antibacterial effect due to the high ion release of copper on the surface, which can inhibit biofilm formation and biocorrosion.

ACC-Deaminase producing Pseudomonas putida RT12 inoculation: A promising strategy for improving Brassica juncea tolerance to salinity stress

An important abiotic stressor that hinders plant growth, nutrient uptake, and global agricultural productivity is soil salinity. Among the different strategies to overcome the issue of salinity in agriculture sector, plant growth-promoting rhizobacteria (PGPR) have gained recognition as promising beneficial microbes that can improve plants’ response to biotic and abiotic stressors. The salinity tolerance and traits that promote plant growth of eight PGPR strains (RT1, RT2, RT3, RT4, RT5, RT7, and RT12) were evaluated in this study. During screening, one strain, RT12, had the highest plant growth-promoting activity and salt tolerance in the group. The strain when subjected to NaCl stress showed quantitative ACC-deaminase activity, in the presence of NaCl at various concentrations, demonstrating extraordinary tolerance to salt stress by withstanding doses of up to 3M NaCl. In order to further investigate the effects of salt stress on Brassica juncea (mustard), RT12, which was identified as Pseudomonas putida using 16s RNA sequencing, was inoculated. Two salt treatments (100 and 150 mM) were applied to the mustard variety ‘Mingora’ in a greenhouse. The results revealed that through ACC utilization, PGPR directly induced plant growth in salt-stressed mustard plants by lowering excess ethylene production. All plant parameters were negatively impacted by an increase in NaCl concentration in uninoculated plants. However, P. putida RT12 inoculation enhanced all growth parameters, antioxidant production, total soluble sugar (TSS), total protein (TP), proline, relative water content (RWC), chlorophyll contents, and nutrient uptake in salt-treated plants. The inoculation with P. putida also caused a marked decline in Na+ uptake and an increase in K+ uptake in the shoot. By maintaining a greater K+/Na+ ratio in the tissues of RT12-inoculated plants compared to controls, this change in ion uptake helped to maintain nutritional balance of the plants. The findings suggest that inoculating plants with ACC deaminase-producing PGPR, such as P. putida RT12, may boost growth and stress resistance.

Degradation of SDS by psychrotolerant Staphylococcus saprophyticus and Bacillus pumilus isolated from Southern Ocean water samples.

Bioremediation of surfactants in water bodies holds significant ecological importance as they are contaminants of emerging concern posing substantial threats to the aquatic environment. Microbes exhibiting special ability in terms of bioremediation of contaminants have always been reported to thrive in extraordinary environmental conditions that can be extreme in terms of temperature, lack of nutrients, and salinity. Therefore, in the present investigation, a total of 46 bacterial isolates were isolated from the Indian sector of the Southern Ocean and screened for degradation of sodium dodecyl sulphate (SDS). Further, two Gram-positive psychrotolerant bacterial strains, ASOI-01 and ASOI-02 were identified with significant SDS degradation potential. These isolates were further studied for growth optimization under different environmental conditions. The strains were characterized as Staphylococcus saprophyticus and Bacillus pumilus based on morphological, biochemical, and molecular (16S RNA gene) characteristics. The study reports 88.9% and 93.4% degradation of SDS at a concentration of 100 mgL-1, at 20°C, and pH 7 by S. saprophyticus ASOI-01 and B. pumilus ASOI-02, respectively. The experiments were also conducted in wastewater samples where a slight reduction in degradation efficiency was observed with strains ASOI-01 and ASOI-02 exhibiting 76.83 and 64.93% degradation of SDS respectively. This study infers that these bacteria can be used for the bioremediation of anionic surfactants from water bodies and establishes the potential of extremophilic microbes for the utilization of sustainable wastewater management.

Identification, characterization and complete genome analysis of a Vibrio anguillarum isolated from Sebastes schlegelii

Vibrio anguillarum is an important fish pathogen in mariculture, which can infect fish with great economic losses. In this study, a Vibrio anguillarum isolated from Sebastes schlegelii was named VA1 and was identified and characterized from aspects of morphology, physiological and biochemical characteristics, 16SRNA, virulence genes, drug sensitivity, and extracellular enzyme activity. At the same time, The VA1 was investigated at the genomic level. The results showed that a Gram-negative was isolated from the diseased fish. The VA1 was characterized with uneven surface and visible flagella wrapped in a sheath and microbubble structures. The VA1 was identified as Vibrio anguillarum based on the 16S RNA sequence and physiological and biochemical characteristics. The VA1 carried most of the virulence genes (24/29) and was resistant to penicillin, oxacillin, ampicillin, cefradine, neomycin, pipemidic acid, ofloxacin, and norfloxacin. The pathogenicity of the isolated strain was confirmed by an experimental analysis, and its LD50 was 6.43 × 106 CFU/ml. The VA1 had the ability to secrete gelatinase, protease, and amylase, and it had α-hemolysis. The whole genome size of the VA1 was 4232328bp and the G + C content was 44.95 %, consisting of two circular chromosomes, Chromosome1 and Chromosome2, with no plasmid. There were 1006 predicted protein coding sequences (CDSs). A total of 526 genes were predicted as virulence-related genes which could be classified as type IV pili, flagella, hemolysin, siderophore, and type VI secretion system. Virulence genes and correlation data were supported with the histopathological examination of the affected organs and tissues. 194 genes were predicted as antibiotic resistance genes, including fluoroquinolone antibiotic, aminoglycoside antibiotic, and beta-lactam resistant genes, which agreed with the results of the above drug sensitivity, indicating VA1 to be a multidrug-resistant bacterium. This study provided a theoretical basis for a better understanding of pathogenicity and antibiotic resistance, which might contribute to the prevention of V. anguillarum in the future.

Multiomic study of the protective mechanism of Persicaria capitata (Buch.-Ham. ex D.Don) H.Gross against streptozotocin-induced diabetic nephropathy in Guizhou miniature pigs

BackgroundPersicaria capitata (Buch.-Ham. ex D.Don) H.Gross (P. capitata, PCB), a traditional drug of the Miao people in China, is potential traditional drug used for the treatment of diabetic nephropathy (DN). PurposeThe purpose of this study is to investigate the function of P. capitata and clarify its protective mechanism against DN. MethodsWe induced DN in the Guizhou miniature pig with injections of streptozotocin, and P. capitata was added to the pigs’ diet to treat DN. In week 16, all the animals were slaughtered, samples were collected, and the relative DN indices were measured. 16S rRNA sequencing, metagenomics, metabolomics, RNA sequencing, and proteomics were used to explore the protective mechanism of P. capitata against DN. ResultsDietary supplementation with P. capitata significantly reduced the extent of the disease, not only in term of the relative disease indices but also in hematoxylin-eosin-stained tissues. A multiomic analysis showed that two microbes (Clostridium baratii and Escherichia coli), five metabolites (oleic acid, linoleic acid, 4-phenylbutyric acid, 18-β-glycyrrhetinic acid, and ergosterol peroxide), four proteins (ENTPD5, EPHX1, ARVCF and TREH), four important mRNAs (encoding ENTPD5, EPHX1, ARVCF, and TREH), six lncRNAs (TCONS_00024194, TCONS_00085825, TCONS_00006937, TCONS_00070981, TCONS_00074099, and TCONS_00097913), and two circRNAs (novel_circ_0001514 and novel_circ_0017507) are all involved in the protective mechanism of P. capitata against DN. ConclusionsOur results provide multidimensional theoretical support for the study and application of P. capitata.

Molecular detection of ‘Candidatus phytoplasma aurantifolia’ associated with virescence and phyllody of Zinnia peruviana: A new record for India

AbstractZinnia peruviana (Asteraceae) is an annual flowering plant cultivated in various gardens of Mysore, the south of Karnataka state, India. During 2021, phytoplasma‐like symptoms such as virescence and phyllody were observed on Zinnia in Mysore local gardens. A total of 10 symptomatic and five asymptomatic samples were collected, and the DNA was amplified by PCR using primers specific to 16S RNA and secA genes. The nucleotide sequence analysis showed that the 16S RNA and SecA gene sequences were most similar to those of ‘Ca. P. aurantifolia’, with identities greater than 99%. The phytoplasma sequence from this study shared a common clade with ‘Ca. P. aurantifolia’ when phylogenetic analysis was done. Similarly, the reference sequences for the 16S rRNA and SecA region confirmed the identity of the phytoplasma associated with the leaves of Zinnia. This is the new host record for ‘Ca. P. aurantifolia’ (16SrII‐D) phytoplasma associated with Z. peruviana from India.

Distribution, diversity and diversification from DNA barcoding perspective: The case of Gammarus radiation in the ancient Lake Ohrid

AbstractAimA detailed, comparative DNA‐barcoding and morphospecies‐based overview of the vertical and horizontal distribution of Lake Ohrid's endemic Gammarus species flock is provided. Re‐evaluation of the time frame for the onset of the species flock and identification of events that putatively influenced diversification processes.LocationLake Ohrid, Balkan Peninsula, Europe.TaxonGammarus species flock (Amphipoda, Crustacea).MethodsExtensive sampling and DNA barcoding of 600 individuals was carried out. DNA sequences were analysed using species delimitation methods, haplotype network reconstructions, Bayesian molecular dating and demographic analyses. The COI‐based species delimitation results were validated with nuclear 28S RNA data.ResultsThe species flock distribution has a weak horizontal but clear vertical structure. The diversity along bathymetric gradients correlates with temperature and salinity; and the highest diversity is observed in sublittoral and springs on the lake's shore. Two new molecular units representing putatively new species are revealed and supported also by the nuclear marker. The onset of flock radiation overlaps with the time of lake formation. The COI gene shows signs of positive selection and an acceleration in substitution rate. The demographic changes within the flock happened during the last thousands years.Main ConclusionsDistribution of the Gammarus species flock is vertically structured, reflecting habitat zonation. Parapatric speciation is one of the possible mechanisms behind the flock's diversification. Detection of new MOTUs suggests that the flock's diversity is still not fully revealed. Simultaneously, failure to collect three previously known MOTUs suggests a loss of gammarid diversity in the lake. This represents, together with the current threats to the lake ecosystem (i.e. climate changes, development of tourism), a clear call for conservation efforts. The speciation events and demographic changes within the flock relate presumably to glacial and postglacial water level changes and to the colonisation of new depth ranges and the associated springs.

Asynchronous application of modified biochar and exogenous fungus Scedosporium sp. ZYY for enhanced degradation of oil-contaminated intertidal mudflat sediment.

Intertidal mudflats are susceptible to oil pollution due to their proximity to discharges from industries, accidental spills from marine shipping activities, oil drilling, pipeline seepages, and river outflows. The experimental study was divided into two periods. In the first period, microcosm trials were carried out to examine the effect of chemically modified biochar on biological hydrocarbon removal from sediments. The modified biochar's surface area increased from 2.544 to 25.378 m2/g, followed by a corresponding increase in the hydrogen-carbon and oxygen-carbon ratio, indicating improved stability and polarity. In the second period, the effect of exogenous fungus - Scedoporium sp. ZYY on the bacterial community structure was examined in relation to total petroleum hydrocarbon (TPH) removal. The maximum TPH removal efficiency of 82.4% was achieved in treatments with the modified biochar, followed by a corresponding increase in Fluorescein diacetate hydrolysis activity. Furthermore, high-throughput 16S RNA gene sequencing employed to identify changes in the bacterial community of the original sediment and treatments before and after fungal inoculation revealed Proteobacteria as the dominant phylum. In addition, it was observed that Scedoporium sp. ZYY promoted the proliferation of specific TPH-degraders, particularly, Hyphomonas adhaerens which accounted for 77% of the total degrading populations in treatments where TPH removal was highest. Findings in this study provide valuable insights into the effect of modified biochar and the fundamental role of exogenous fungus towards the effective degradation of oil-contaminated intertidal mudflat sediments.

Cryo-EMstructure of SRP68/72 reveals an extended dimerization domain with RNA-binding activity.

The signal recognition particle (SRP) is a critical component in protein sorting pathways in all domains of life. Human SRP contains six proteins bound to the 7S RNA and their structures and functions have been mostly elucidated. The SRP68/72 dimer is the largest SRP component and is essential for SRP function. Although the structures of the SRP68/72 RNA binding and dimerization domains have been previously reported, the structure and function of large portions of the SRP68/72 dimer remain unknown. Here, we analyse full-length SRP68/72 using cryo-EM and report that SRP68/72 depend on each other for stability and form an extended dimerization domain. This newly observed dimerization domain is both a protein- and RNA-binding domain. Comparative analysis with current structural models suggests that this dimerization domain undergoes dramatic translocation upon SRP docking onto SRP receptor and eventually comes close to the Alu domain. We propose that the SRP68/72 dimerization domain functions by binding and detaching the Alu domain and SRP9/14 from the ribosomal surface, thus releasing elongation arrest upon docking onto the ER membrane.

RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria.

Bacteria have evolved structured RNAs that can associate with RNA polymerase (RNAP). Two of them have been known so far-6S RNA and Ms1 RNA but it is unclear if any other types of RNAs binding to RNAP exist in bacteria. To identify all RNAs interacting with RNAP and the primary σ factors, we have established and performed native RIP-seq in Bacillus subtilis, Corynebacterium glutamicum, Streptomyces coelicolor, Mycobacterium smegmatis and the pathogenic Mycobacterium tuberculosis. Besides known 6S RNAs in B. subtilis and Ms1 in M. smegmatis, we detected MTS2823, a homologue of Ms1, on RNAP in M. tuberculosis. In C. glutamicum, we discovered novel types of structured RNAs that associate with RNAP. Furthermore, we identified other species-specific RNAs including full-length mRNAs, revealing a previously unknown landscape of RNAs interacting with the bacterial transcription machinery.

Gut bacterial community of Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Crambidae) is driven by rice varieties

AbstractTo understand the effect of diet on gut bacteria of Cnaphalocrocis medinalis (rice leaf folder, RLF), we compared the composition and diversity of gut bacterial community in C. medinalis larvae collected from three different rice variety fields of Minghui 82 (RLF1), Youngyong 15 (RLF2) and Minghui 2155 (RLF3), using culture‐independent PCR (V3 variable region)‐denaturing gradient gel electrophoresis (PCR‐DGGE) methods and hypervariable region (V4) of 16S rRNA sequenced by Illumina HiSeq platform. The DGGE result showed that the bacteria genera Asaia, Bacillus, Stenotrophomonas, Achromobacter and Serratia coexisted in the guts of RLF1, RLF2 and RLF3, while Cedecea, Burkholderia and Acinetobacter coexisted in the guts of RLF2 and RLF3. However, only the genus Enterococcus existed in the guts of RLF1, and Pantoea, Wolbachia and Tumebacillus in RLF3 larvae. A total of 25 bacterial phyla, 48 classes, 127 orders, 223 families, and 406 genera were identified when using 16s RNA sequencing, with 35 genera coexisted in RLF1, RLF2 and RLF3 larval guts, while 83, 36, 141 unique genera existed in RLF1, RLF2 and RLF3, respectively. The indices of ACE and Shannon were not significantly different among RLF1, RLF2 and RLF3. The dominant bacterial taxa were Proteobacteria, Bacteroidetes and Firmicutes at the phylum level, and Acinetobacter and Wolbachia at the genus level. The relative genus abundance for the genera with relative abundance (≥0.01) was significantly different among RLF1, RLF2 and RLF3. The findings indicated that different rice varieties had significant effects on the relative abundance of gut bacteria in RLF, which could provide new insights into the relationship between insect gut bacteria and their associated host plants.

16S rRNA Next-Generation Sequencing May Not Be Useful for Examining Suspected Cases of Spontaneous Bacterial Peritonitis.

Background and Objectives: Ascites, often associated with liver cirrhosis, poses diagnostic challenges, particularly in detecting bacterial infections. Traditional methods have limitations, prompting the exploration of advanced techniques such as 16S rDNA next-generation sequencing (NGS) for improved diagnostics in such low-biomass fluids. The aim of this study was to investigate whether the NGS method enhances detection sensitivity compared to a conventional ascites culture. Additionally, we aimed to explore the presence of a microbiome in the abdominal cavity and determine whether it has a sterile condition. Materials and Methods: Ten patients with clinically suspected spontaneous bacterial peritonitis (SBP) were included in this study. A traditional ascites culture was performed, and all ascites samples were subjected to 16S ribosomal RNA gene amplification and sequencing. 16S rRNA gene sequencing results were interpreted by comparing them to positive and negative controls for each sample. Results: Differential centrifugation was applied to all ascites samples, resulting in very small or no bacterial pellets being harvested. The examination of the 16S amplicon sequencing libraries indicated that the target amplicon products were either minimally visible or exhibited lower intensity than their corresponding negative controls. Contaminants present in the reagents were also identified in the ascites samples. Sequence analysis of the 16S rRNA gene of all samples showed microbial compositions that were akin to those found in the negative controls, without any bacteria isolated that were unique to the samples. Conclusions: The peritoneal cavity and ascites exhibit low bacterial biomass even in the presence of SBP, resulting in a very low positivity rate in 16S rRNA gene sequencing. Hence, the 16S RNA sequencing method does little to enhance the rate of positive samples compared to traditional culture methods, including in SBP cases.

Geographic distribution of bacterial communities of inland waters in China

Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.