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Anaerobe Aug 2023Members of the Actinomyces genus and Actinomyces-like organisms (ALOs; namely Actinotignum, Arcanobacterium, Schaalia and Varibaculum) are Gram-positive,... (Review)
Review
Members of the Actinomyces genus and Actinomyces-like organisms (ALOs; namely Actinotignum, Arcanobacterium, Schaalia and Varibaculum) are Gram-positive, non-spore-forming rods that are commensal members of the human oral cavity, gastrointestinal tract, female genital tract and skin microbiota. Cervicofacial actinomycosis or "lumpy jaw syndrome" - the chronic, suppurative granulomatous disease caused by Actinomyces spp. And ALOs - is characterized by an initially slow and unspecific disease-presentation, which often mimics other pathologies, followed by the formation of painful abscesses and severe tissue destruction. Actinomycosis has been described as a rare disease, however, reliable epidemiological data are lacking. In addition, there is increasing awareness regarding the role of Actinomyces spp. in the development of osteoradionecrosis and medication-related osteonecrosis of the jaw. The aim of this narrative review is to succinctly summarize the current advances regarding the microbiological, clinical, diagnostic and therapeutic aspects of cervicofacial actinomycosis, in addition to the roles of Actinomyces species and ALOs as members of the oral microbiota and in dental biofilm, in other dental infections (caries, root canal infection, periapical infection, periodontitis) and osteonecrosis of the jaw, in the context of recent taxonomic changes affecting the genus. Our paper aims to be a blueprint for dentists, other physicians, microbiologists and researchers regarding the multifaceted field of cervicofacial actinomycosis.
Topics: Female; Humans; Actinomyces; Actinomycosis; Actinomycosis, Cervicofacial; Mouth; Actinomycetaceae; Osteonecrosis
PubMed: 37482285
DOI: 10.1016/j.anaerobe.2023.102767 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Nov 2023Cyclodipeptide (CDP) composed of two amino acids is the simplest cyclic peptide. These two amino acids form a typical diketopiperazine (DKP) ring by linking each other... (Review)
Review
Cyclodipeptide (CDP) composed of two amino acids is the simplest cyclic peptide. These two amino acids form a typical diketopiperazine (DKP) ring by linking each other with peptide bonds. This characteristic stable ring skeleton is the foundation of CDP to display extensive and excellent bioactivities, which is beneficial for CDPs' pharmaceutical research and development. The natural CDP products are well isolated from actinomycetes. These bacteria can synthesize DKP backbones with nonribosomal peptide synthetase (NRPS) or cyclodipeptide synthase (CDPS). Moreover, actinomycetes could produce a variety of CDPs through different enzymatic modification. The presence of these abundant and diversified catalysis indicates that actinomycetes are promising microbial resource for exploring CDPs. This review summarized the pathways for DKP backbones biosynthesis and their post-modification mechanism in actinomycetes. The aim of this review was to accelerate the genome mining of CDPs and their isolation, purification and structure identification, and to facilitate revealing the biosynthesis mechanism of novel CDPs as well as their synthetic biology design.
Topics: Actinobacteria; Actinomyces; Biological Products; Bacteria; Diketopiperazines; Amino Acids
PubMed: 38013180
DOI: 10.13345/j.cjb.230068 -
Frontiers in Cellular and Infection... 2024Numerous studies have demonstrated the influence of gut microbiota on the development of obesity. In this study, we utilized Mendelian randomization (MR) analysis to...
BACKGROUND
Numerous studies have demonstrated the influence of gut microbiota on the development of obesity. In this study, we utilized Mendelian randomization (MR) analysis to investigate the gut microbiota characteristics among different types of obese patients, aiming to elucidate the underlying mechanisms and provide novel insights for obesity treatment.
METHODS
Two-sample multivariable Mendelian randomization (MR) analysis was employed to assess causal relationships between gut microbiota and various obesity subtypes. Gut microbiota data were obtained from the international consortium MiBioGen, and data on obese individuals were sourced from the Finnish National Biobank FinnGen. Eligible single-nucleotide polymorphisms (SNPs) were selected as instrumental variables. Various analytical methods, including inverse variance weighted (IVW), MR-Egger regression, weighted median, MR-RAPS, and Lasso regression, were applied. Sensitivity analyses for quality control included MR-Egger intercept tests, Cochran's Q tests, and leave-one-out analyses and others.
RESULTS
Mendelian randomization studies revealed distinct gut microbiota profiles among European populations with different obesity subtypes. Following multivariable MR analysis, we found that [: 0.842, : 0.766-0.926, Adjusted value: 0.028] independently reduced the risk of obesity induced by excessive calorie intake, while [: 4.252, : 2.177-8.307, Adjusted value: 0.002] independently increased the risk of medication-induced obesity. For localized adiposity, [: 0.213, : 0.115-0.395, Adjusted value: <0.001] acted as a protective factor. In the case of extreme obesity with alveolar hypoventilation, [: 0.724, : 0.609-0.860, Adjusted value: 0.035] reduced the risk of its occurrence. Additionally, six gut microbiota may have potential roles in the onset of different types of obesity. Specifically, the torques group may increase the risk of its occurrence. and may serve as protective factors in the onset of Drug-induced obesity. , , and , on the other hand, could potentially increase the risk of Drug-induced obesity. No evidence of heterogeneity or horizontal pleiotropy among SNPs was found in the above studies (all values for Q test and MR-Egger intercept > 0.05).
CONCLUSION
Gut microbiota abundance is causally related to obesity, with distinct gut microbiota profiles observed among different obesity subtypes. Four bacterial species, including , , and independently influence the development of various types of obesity. Probiotic and prebiotic supplementation may represent a novel approach in future obesity management.
Topics: Humans; Gastrointestinal Microbiome; Obesity; Actinomycetaceae; Bacteroidetes; Clostridiales; Lactobacillus; Nonoxynol; Genome-Wide Association Study
PubMed: 38375360
DOI: 10.3389/fcimb.2024.1352109 -
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 -
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 -
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 -
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 -
Microbiology (Reading, England) Nov 2023In the search for novel therapeutics to combat the ongoing antimicrobial resistance crisis, scientists are turning to underexplored environments. Defensive mutualisms...
In the search for novel therapeutics to combat the ongoing antimicrobial resistance crisis, scientists are turning to underexplored environments. Defensive mutualisms between hymenopteran insects and actinomycetes represent important reservoirs for bioactive compounds. In this study, we examined the association between actinomycetes and ant-plants spanning three different ant and plant species combinations (, and ). Eight plants were sampled including four containing three containing and a single plant containing . A total of 47 actinomycetes were obtained from the sampled material, with 5, 16, and 26 isolates originating from cuticle, tissue, and nest samples, respectively. Cross-streaking tests showed that 12 out of 47 isolates inhibited bacterial pathogens. The most frequently inhibited pathogens in the cross-streaking tests were and while was the least inhibited. Among the three primary screening media used, ISP2 agar was the most suitable for secondary metabolism as more isolates exhibited antibacterial activity when grown on the medium. TFS2010 and TFS2003, which matched to (>99% similarity), were the most bioactive isolates in cross-streaking tests. TFS2010 displayed the strong antibacterial on Nutrient agar, Mueller Hinton agar, and ISP2 agar while TFS2003 only exhibited strong antibacterial activity on Nutrient agar. Furthermore, a difference in potency of extracts based on batch culture medium was noted in TFS2010 DNA was extracted from 19 isolates and followed by 16SrRNA gene sequencing. Analysis of sequence data revealed the presence of six genera, including , , , , , and , with the latter being the most abundant taxon. Among these, three isolates (PNS3002, PNS3005, and TFS3001) are likely to represent new species while one (TFS2015) is likely to be a member of a novel genus. Our work represents the first attempt to study actinomycetes from -ant mutualisms.
Topics: Animals; Actinobacteria; Actinomyces; Ants; Agar; Staphylococcus aureus; Escherichia coli; Anti-Bacterial Agents
PubMed: 37938888
DOI: 10.1099/mic.0.001410 -
Journal of Periodontology Jun 2024This study determined the prevalence of aggressive (molar-incisor pattern) (Ag/MI) periodontitis and assessed the associated subgingival bacterial-herpesvirus microbiota...
BACKGROUND
This study determined the prevalence of aggressive (molar-incisor pattern) (Ag/MI) periodontitis and assessed the associated subgingival bacterial-herpesvirus microbiota in Pueblo Indian adolescents in the southwestern United States.
METHODS
The study included 240 Pueblo Indian adolescents, aged 13-20 years old, residing in three Rio Grande River villages in New Mexico and the Hopi Pueblo reservation in Arizona. Adolescents with Ag/MI periodontitis or periodontal health provided subgingival samples for culture of bacterial pathogens and for polymerase chain reaction detection of periodontal herpesviruses.
RESULTS
Ag/MI periodontitis was detected in 22 (9.2%) Pueblo Indian adolescents, with 21 exhibiting a localized molar-incisor breakdown pattern. Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and other red/orange complex bacterial pathogens predominated in Ag/MI periodontitis, whereas periodontal health yielded mainly viridans streptococci and Actinomyces species. Periodontal herpesviruses demonstrated a 3.5 odds ratio relationship with Ag/MI periodontitis. The only adolescent with generalized Ag/MI periodontitis harbored viral co-infection by cytomegalovirus plus Epstein-Barr virus Type 1, in addition to A. actinomycetemcomitans, P. gingivalis, and several other periodontopathic bacteria.
CONCLUSIONS
Pueblo Indian adolescents showed an unusually high prevalence of early-age Ag/MI periodontitis predominated by periodontopathic bacteria and herpesviruses suspected to be major etiologic agents of the disease.
Topics: Humans; Adolescent; Young Adult; Male; Female; Aggressive Periodontitis; Indians, North American; Aggregatibacter actinomycetemcomitans; Porphyromonas gingivalis; Arizona; New Mexico; Cytomegalovirus; Actinomyces; Viridans Streptococci; Prevalence; Coinfection; Herpesvirus 4, Human; Herpesviridae
PubMed: 37910464
DOI: 10.1002/JPER.23-0410 -
Frontiers in Microbiology 2023Enteric dysbacteriosis is strongly associated with nonalcoholic fatty liver disease (NAFLD). However, the underlying causal relationship remains unknown. Thus, the...
INTRODUCTION
Enteric dysbacteriosis is strongly associated with nonalcoholic fatty liver disease (NAFLD). However, the underlying causal relationship remains unknown. Thus, the present study aimed to investigate the relationship between gut microbiota and NAFLD using Mendelian randomization (MR) and analyze the target genes potentially regulated by specific microbiota.
METHODS
Bidirectional two-sample MR analysis was performed using inverse variance weighted (IVW) supplemented by MR-Egger, weighted median, simple mode, and weighted mode methods. Data were pooled from gut microbiota and NAFLD association studies. The least absolute shrinkage, selection operator regression, and the Support Vector Machine algorithm were used to identify genes regulated by these intestinal flora in NAFLD. The liver expression of these genes was verified in methionine choline-deficient (MCD) diet-fed mice.
RESULTS
IVW results confirmed a causal relationship between eight specific gut microbes and NAFLD. Notably, the order Actinomycetales, NB1n, the family Actinomycetaceae, Oxalobacteraceae and the genus were positively correlated, whereas Lactobacillaceae, the , and were negatively correlated with NAFLD onset. In NAFLD, these eight bacteria regulated four genes: colony-stimulating factor 2 receptor β, fucosyltransferase 2, 17-beta-hydroxysteroid dehydrogenase 14, and microtubule affinity regulatory kinase 3 (). All genes, except , were differentially expressed in the liver tissues of MCD diet-fed mice.
DISCUSSION
The abundance of eight gut microbiota species and NAFLD progression displayed a causal relationship based on the expression of the four target genes. Our findings contributed to the advancement of intestinal microecology-based diagnostic technologies and targeted therapies for NAFLD.
PubMed: 38260910
DOI: 10.3389/fmicb.2023.1320279