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Communications Biology Jan 2024The nasal cavity harbors diverse microbiota that contributes to human health and respiratory diseases. However, whether and to what extent the host genome shapes the...
The nasal cavity harbors diverse microbiota that contributes to human health and respiratory diseases. However, whether and to what extent the host genome shapes the nasal microbiome remains largely unknown. Here, by dissecting the human genome and nasal metagenome data from 1401 healthy individuals, we demonstrated that the top three host genetic principal components strongly correlated with the nasal microbiota diversity and composition. The genetic association analyses identified 63 genome-wide significant loci affecting the nasal microbial taxa and functions, of which 2 loci reached study-wide significance (p < 1.7 × 10): rs73268759 within CAMK2A associated with genus Actinomyces and family Actinomycetaceae; and rs35211877 near POM121L12 with Gemella asaccharolytica. In addition to respiratory-related diseases, the associated loci are mainly implicated in cardiometabolic or neuropsychiatric diseases. Functional analysis showed the associated genes were most significantly expressed in the nasal airway epithelium tissue and enriched in the calcium signaling and hippo signaling pathway. Further observational correlation and Mendelian randomization analyses consistently suggested the causal effects of Serratia grimesii and Yokenella regensburgei on cardiometabolic biomarkers (cystine, glutamic acid, and creatine). This study suggested that the host genome plays an important role in shaping the nasal microbiome.
Topics: Humans; Genome-Wide Association Study; Nose; Microbiota; Genetic Variation; Cardiovascular Diseases
PubMed: 38291185
DOI: 10.1038/s42003-024-05822-5 -
Archives of Iranian Medicine Jun 2022
Topics: Actinomyces; Empyema, Pleural; Humans; Lung Abscess
PubMed: 35943021
DOI: 10.34172/aim.2022.65 -
Frontiers in Cellular and Infection... 2023Four Gram-staining-positive, aerobic, non-motile, circle-shaped bacteria were isolated from the faeces of bats ( and ) collected from Guangxi autonomous region...
Four Gram-staining-positive, aerobic, non-motile, circle-shaped bacteria were isolated from the faeces of bats ( and ) collected from Guangxi autonomous region (E106°49'20″, N22°20'54″) and Yunnan province (E102°04'39″, N25°09'10″) of South China. Strains HY006 and HY008 shared highly 16S rRNA gene sequence similarity to those of W204 (99.3%) and CPCC 203535 (97.3%), while the strains HY1745 and HY1793 were closest to the type strains H23M54 (98.7%), CFH 30183 (98.3%), and 01-Gi-040 (98.1%). Furthermore, when compared to the other members of the genus , the digital DNA-DNA hybridization and average nucleotide identity values of the four novel strains were within the ranges of 19.6-33.7% and 70.6-87.4%, respectively, both of which were below the respective recommended cutoff values of 70.0% and 95-96%. Significantly, strain HY006 was resistant to chloramphenicol and linezolid whereas strain HY1793 was resistant to erythromycin, clindamycin (intermediately), and levofloxacin (intermediately). The main cellular fatty acids (>20.0%) of our isolates were -C and -C. Strains HY006 and HY1793 contained ornithine as the diagnostic diamino acid, also along with the alanine, glycine and glutamic acid in their cell wall. Based on phylogenetic, chemotaxonomic and phenotypic analyses, these four strains could be classified as two novel species of the genus , for which the names sp. nov. and sp. nov. are proposed. The type strains are HY006 (=CGMCC 1.16565 =JCM 33397) and HY1793 (=CGMCC 1.19143 =JCM 34881), respectively.
Topics: Animals; Actinobacteria; Actinomyces; Chiroptera; Phylogeny; RNA, Ribosomal, 16S; China; Genomics; Feces; DNA
PubMed: 36864884
DOI: 10.3389/fcimb.2023.1093407 -
International Journal of Systematic and... Jul 2023Filamentous actinomycetes, designated SL13 and SL54, were isolated from pine litter and their taxonomic status resolved using a polyphasic approach. The isolates exhibit...
sp. nov., acidotolerant actinomycetes from pine litter, reclassification of , , and as comb. nov., comb. nov., comb. nov. and comb. nov., and emended descriptions of the genus , the family and .
Filamentous actinomycetes, designated SL13 and SL54, were isolated from pine litter and their taxonomic status resolved using a polyphasic approach. The isolates exhibit chemotaxonomic and morphological properties consistent with their classification in the family . They form extensively branched substrate mycelia bearing aerial hyphae that differentiate into straight chains of cylindrical spores. The whole-organism hydrolysates contain ll-diaminopimelic acid, glucose, mannose and ribose, the predominant isoprenologue is MK-9(H), the polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and glycophospholipids, and the major fatty acids are anteiso-C, iso-C, iso-C and anteiso-C. Phylogenetic trees based on 16S rRNA gene sequences and multilocus gene sequences of conserved housekeeping genes show that the isolates form a well-supported lineage that is most closely related to NBRC 115203. All of these strains form a well-defined clade in the multilocus sequence analysis tree together with DSM 46488, DSM 41836 and DSM 42083. Draft genomes assemblies of the isolates are rich in biosynthetic gene clusters predicted to produce novel specialized metabolites and stress-related genes which provide an insight into how they have adapted to the harsh conditions that prevail in pine litter. Phylogenomically, both isolates belong to the same lineage as the type strains of , , and ; these relationships are underpinned by high average amino acid identity, average nucleotide identity and genomic DNA-DNA hybridization values. These metrics confirm that isolates SL13 and SL54 belong to a novel species that is most closely related to NBRC 115203 and that these strains together with DSM 41836, DSM 42083 belong to the genus . Consequently, it is proposed that the isolates be recognized as a new species, comb. nov., with isolate SL54 (=DSM 111111=PCM3044) as the type strain, and that , and be transferred to the genus as comb. nov., comb. nov. and comb. nov. Emended descriptions are given for the genus , the family and for which was found to be a close relative of the isolates in the 16S rRNA gene sequence analyses. It is also proposed that be transferred to the genus as comb. nov based on its position in the MLSA and phylogenomic trees and associated genomic data.
Topics: Actinobacteria; Actinomyces; Phylogeny; RNA, Ribosomal, 16S; Fatty Acids; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Base Composition; Streptomyces; Streptomycetaceae; Phospholipids
PubMed: 37486349
DOI: 10.1099/ijsem.0.005978 -
BJU International Jan 2022To undertake the first comprehensive evaluation of the urinary microbiota associated with Hunner lesion (HL) interstitial cystitis/bladder pain syndrome (IC/BPS)....
OBJECTIVE
To undertake the first comprehensive evaluation of the urinary microbiota associated with Hunner lesion (HL) interstitial cystitis/bladder pain syndrome (IC/BPS). Despite no previous identification of a distinct IC/BPS microbial urotype, HL IC/BPS, an inflammatory subtype of IC/BPS, was hypothesized most likely to be associated with a specific bacterial species or microbial pattern.
PARTICIPANTS AND METHODS
The bacterial microbiota of midstream urine specimens from HL IC/BPS and age- and gender-matched IC/BPS patients without HL (non-HL IC/BPS) were examined using the pan-bacterial domain clinical-level molecular diagnostic Pacific Biosciences full-length 16S gene sequencing protocol, informatics pipeline and database. We characterized the differential presence, abundances, and diversity of species, as well as gender-specific differences between and among HL and non-HL IC/BPS patients.
RESULTS
A total of 59 patients with IC/BPS were enrolled (29 HL, 30 non-HL; 43 women, 16 men) from a single centre and the microbiota in midstream urine specimens was available for comparison. The species abundance differentiation between the HL and non-HL groups (12 species) was not significantly different after Bonferroni adjustments for multiple comparisons. Similarly, the nine differentiating species noted between female HL and non-HL patients were not significantly different after similar statistical correction. However, four species abundances (out of the 10 species differences identified prior to correction) remained significantly different between male HL and non-HL subjects: Negativicoccus succinivorans, Porphyromonas somerae, Mobiluncus curtisii and Corynebacterium renale. Shannon diversity metrics showed significantly higher diversity among HL male patients than HL female patients (P = 0.045), but no significant diversity differences between HL and non-HL patients overall.
CONCLUSIONS
We were not able to identify a unique pathogenic urinary microbiota that differentiates all HL from all non-HL IC/BPS. It is likely that the male-specific differences resulted from colonization/contamination remote from the bladder. We were not able to show that bacteria play an important role in patients with HL IC/BPS.
Topics: Adult; Aged; Aged, 80 and over; Bacteria; Corynebacterium; Cystitis, Interstitial; DNA, Bacterial; Female; Humans; Male; Microbiota; Middle Aged; Mobiluncus; Porphyromonas; Sex Factors; Urine; Veillonellaceae
PubMed: 34143561
DOI: 10.1111/bju.15519 -
Frontiers in Microbiology 2022Our previous research reported that supplementation of DSM 25841 promoted growth and disease resistance of weaned pigs under enterotoxigenic (ETEC) challenge and its...
Our previous research reported that supplementation of DSM 25841 promoted growth and disease resistance of weaned pigs under enterotoxigenic (ETEC) challenge and its efficacy is comparable to carbadox. This follow-up study aimed to characterize the effects of ETEC infection, supplementing DSM 25841 or carbadox on intestinal microbiota of pigs. Forty-eight weaned pigs (6.17 ± 0.36 kg BW) were randomly allotted to one of four treatments: negative control (NC), positive control (PC), antibiotics (AGP, 50 mg/kg of carbadox), and direct fed microbials (DFM, 2.56 × 10 CFU/kg of ). The experiment lasted 28 days with 7 days before and 21 days after first inoculation (day 0). Pigs in the PC, AGP, and DFM groups were orally inoculated with F18 ETEC for 3 consecutive days with 10 CFU per dose per day. Fecal samples were collected on day -7, and day 7 and day 21 post inoculation, digesta samples were collected from jejunum, ileum, and distal colon on day 21 post inoculation to perform 16S rRNA sequencing. Sampling days and locations influenced ( < 0.05) Chao1 index and beta-diversity. Age increased ( < 0.05) the relative abundance of Firmicutes but decreased ( < 0.05) the relative abundance of Bacteroidetes in feces. ETEC infection increased ( < 0.05) the relative abundance of Proteobacteria in feces on day 7 post inoculation. AGP reduced ( < 0.05) relative abundance of Firmicutes and in feces compared with PC and DFM. AGP reduced ( < 0.05) relative abundance of in jejunum and ileum, while DFM reduced ( < 0.05) relative abundance of in jejunum and in ileum, compared with PC. Pigs fed with DFM had greater ( < 0.05) relative abundance of , , in jejunum, in ileum and colon, and in colon than pigs in AGP. Current results indicate that carbadox or had stronger influences on microbial diversity and composition in ileum than other intestinal segments and feces. Supplementation of could increase or maintain the relative abundance of beneficial bacteria in ileum compared with carbadox.
PubMed: 36620005
DOI: 10.3389/fmicb.2022.1064328 -
Molecules (Basel, Switzerland) Mar 2024During the life activities of microorganisms, a variety of secondary metabolites are produced, including antimicrobials and antitumor drugs, which are widely used in... (Review)
Review
During the life activities of microorganisms, a variety of secondary metabolites are produced, including antimicrobials and antitumor drugs, which are widely used in clinical practice. In addition to exploring new antibiotics, this makes it one of the research priorities of to effectively increase the yield of antibiotics in production strains by various means. Most antibiotic-producing strains have a variety of functional regulatory factors that regulate their growth, development, and secondary metabolite biosynthesis processes. Through the study of precursor substances in antibiotic biosynthesis, researchers have revealed the precursor biosynthesis process and the mechanism by which precursor synthesis regulators affect the biosynthesis of secondary metabolites, which can be used to obtain engineered strains with high antibiotic production. This paper summarizes the supply of antibiotic biosynthesis precursors and the progress of research on the role of regulators in the process of precursors in biosynthesis. This lays the foundation for the establishment of effective breeding methods to improve antibiotic yields through the manipulation of precursor synthesis genes and related regulators.
Topics: Anti-Bacterial Agents; Actinobacteria; Actinomyces; Secondary Metabolism
PubMed: 38474644
DOI: 10.3390/molecules29051132 -
Chemosphere Nov 2021Remediation of contaminated water and wastewater using biosorption methods has attracted significant attention in recent decades due to its efficiency, convenience and...
Remediation of contaminated water and wastewater using biosorption methods has attracted significant attention in recent decades due to its efficiency, convenience and minimised environmental effects. Bacterial biosorbents are normally deployed as a non-living powder or suspension. Little is known about the mechanisms or rates of bacterial attachment to surfaces and effect of various conditions on the biofilm development, as well as efficiency of living biofilms in the removal of heavy metals. In the present study, the effect of environmental and nutritional conditions such as pH, temperature, concentrations of phosphate, glucose, amino acid, nitrate, calcium and magnesium, on planktonic and biofilm growth of single and mixed bacterial cultures, were measured. Actinomyces meyeri, Bacillus cereus, Escherichia coli, Pseudomonas fluorescens strains were evaluated to determine the optimum biofilm growth conditions. The Cd(II) biosorption efficiencies of the mixed-species biofilm developed in the optimum growth condition, were investigated and modelled using Langmuir, Freundlich and Dubnin Radushkevich models. The biofilm quantification techniques revealed that the optimum concentration of phosphate, glucose, amino acid, nitrate, calcium and magnesium for the biofilm development were 25, 10, 1, 1.5, 5 and 0.5 g L, respectively. Further increases in the nutrient concentrations resulted in less biofilm growth. The optimum pH for the biofilm growth was 7 and alkaline or acidic conditions caused significant negative effects on the bacterial attachment and development. The optimum temperatures for the bacterial attachment to the surface were between 25 and 35 °C. The maximum Cd(II) biosorption efficiency (99%) and capacity (18.19 mg g) of the mixed-species biofilm, occurred on day 35 (C = 0.1 mg L) and 1 (C = 20 mg L) of biofilm growth, respectively. Modelling of the biosorption data revealed that Cd(II) removal by the living biofilm was a physical process by a monolayer of biofilm. The results of present study suggested that environmental and nutritional conditions had a significant effect on bacterial biofilm formation and its efficiency in Cd(II) removal.
Topics: Actinomycetaceae; Adsorption; Bacillus cereus; Biofilms; Cadmium; Hydrogen-Ion Concentration; Kinetics
PubMed: 34147985
DOI: 10.1016/j.chemosphere.2021.131152 -
Metabolic Engineering Sep 2021Actinomycetes are recognized as excellent producers of microbial natural products, which have a wide range of applications, especially in medicine, agriculture and... (Review)
Review
Actinomycetes are recognized as excellent producers of microbial natural products, which have a wide range of applications, especially in medicine, agriculture and stockbreeding. The three main indexes of industrialization (titer, purity and stability) must be taken into overall consideration in the manufacturing process of natural products. Over the past decades, synthetic biology techniques have expedited the development of industrially competitive strains with excellent performances. Here, we summarize various rational engineering strategies for upgrading the performance of industrial actinomycetes, which include enhancing the yield of natural products, eliminating the by-products and improving the genetic stability of engineered strains. Furthermore, the current challenges and future perspectives for optimizing the industrial strains more systematically through combinatorial engineering strategies are also discussed.
Topics: Actinobacteria; Actinomyces; Biological Products; Metabolic Engineering; Synthetic Biology
PubMed: 34166765
DOI: 10.1016/j.ymben.2021.06.003 -
Trends in Biotechnology Sep 2023Traditional strain breeding of industrial filamentous actinomycetes has long been hampered by insufficient screening throughput. From microtiter plate based methods to...
Traditional strain breeding of industrial filamentous actinomycetes has long been hampered by insufficient screening throughput. From microtiter plate based methods to droplet-based microfluidic screening, various novel product-driven high-throughput screening (HTS) methods have pushed the screening speed limit towards a minimum of hundreds of strains per second with single cell resolution.
Topics: Actinobacteria; Actinomyces; High-Throughput Screening Assays; Microfluidics; Bioreactors
PubMed: 36863908
DOI: 10.1016/j.tibtech.2023.02.004