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Applied Microbiology and Biotechnology Jun 2024Despite increased attention to the aquaculture environment, there is still a lack of understanding regarding the significance of water quality. To address this knowledge...
Despite increased attention to the aquaculture environment, there is still a lack of understanding regarding the significance of water quality. To address this knowledge gap, this study utilized high-throughput sequencing of 16S rRNA and 18S rRNA to examine microbial communities (bacteria and eukaryotes) in coastal water over different months through long-term observations. The goal was to explore interaction patterns in the microbial community and identify potential pathogenic bacteria and red tide organisms. The results revealed significant differences in composition, diversity, and richness of bacterial and eukaryotic operational taxonomic units (OTUs) across various months. Principal coordinate analysis (PCoA) demonstrated distinct temporal variations in bacterial and eukaryotic communities, with significant differences (P = 0.001) among four groups: F (January-April), M (May), S (June-September), and T (October-December). Moreover, a strong association was observed between microbial communities and months, with most OTUs showing a distinct temporal preference. The Kruskal-Wallis test (P < 0.05) indicated significant differences in dominant bacterial and eukaryotic taxa among months, with each group exhibiting unique dominant taxa, including potential pathogenic bacteria and red tide organisms. These findings emphasize the importance of monitoring changes in potentially harmful microorganisms in aquaculture. Network analysis highlighted positive correlations between bacteria and eukaryotes, with bacteria playing a key role in network interactions. The key bacterial genera associated with other microorganisms varied significantly (P < 0.05) across different groups. In summary, this study deepens the understanding of aquaculture water quality and offers valuable insights for maintaining healthy aquaculture practices. KEY POINTS: • Bacterial and eukaryotic communities displayed distinct temporal variations. • Different months exhibited unique potential pathogenic bacteria and red tide organisms. • Bacteria are key taxonomic taxa involved in microbial network interactions.
Topics: Bacteria; Aquaculture; RNA, Ribosomal, 16S; Eukaryota; Seawater; RNA, Ribosomal, 18S; High-Throughput Nucleotide Sequencing; Microbiota; Seasons; Biodiversity; Phylogeny
PubMed: 38900314
DOI: 10.1007/s00253-024-13176-5 -
Microbiology Spectrum Jun 2024DNA fragmentation index (DFI), a new biomarker to diagnose male infertility, is closely associated with poor reproductive outcomes. Previous research reported that...
DNA fragmentation index (DFI), a new biomarker to diagnose male infertility, is closely associated with poor reproductive outcomes. Previous research reported that seminal microbiome correlated with sperm DNA integrity, suggesting that the microbiome may be one of the causes of DNA damage in sperm. However, it has not been elucidated how the microbiota exerts their effects. Here, we used a combination of 16S rRNA sequencing and untargeted metabolomics techniques to investigate the role of microbiota in high sperm DNA fragmentation index (HDFI). We report that increased specific microbial profiles contribute to high sperm DNA fragmentation, thus implicating the seminal microbiome as a new therapeutic target for HDFI patients. Additionally, we found that the amount of species was altered: was enriched in HDFI patients, shedding light on the potential influence of on male reproductive health. Finally, we also identified enrichment of the acetyl-CoA fermentation to butanoate II and purine nucleobase degradation I in the high sperm DNA fragmentation samples, suggesting that butanoate may be the target metabolite of sperm DNA damage. These findings provide valuable insights into the complex interplay between microbiota and sperm quality in HDFI patients, laying the foundation for further research and potential clinical interventions.IMPORTANCEThe DNA fragmentation index (DFI) is a measure of sperm DNA fragmentation. Because high sperm DNA fragmentation index (HDFI) has been strongly associated with adverse reproductive outcomes, this has been linked to the seminal microbiome. Because the number of current treatments for HDFI is limited and most of them have no clear efficacy, it is critical to understand how semen microbiome exerts their effects on sperm DNA. Here, we evaluated the semen microbiome and its metabolites in patients with high and low sperm DNA fragmentation. We found that increased specific microbial profiles contribute to high sperm DNA fragmentation. In particular, was uniquely correlated with high sperm DNA fragmentation. Additionally, butanoate may be the target metabolite produced by the microbiome to damage sperm DNA. Our findings support the interaction between semen microbiome and sperm DNA damage and suggest that seminal microbiome should be a new therapeutic target for HDFI patients.
PubMed: 38899893
DOI: 10.1128/spectrum.00759-24 -
Skin Research and Technology : Official... Jun 2024Ultraviolet (UV)-induced fluorescence technology is widely used in dermatology to identify microbial infections. Our clinical observations under an ultraviolet-induced...
BACKGROUND
Ultraviolet (UV)-induced fluorescence technology is widely used in dermatology to identify microbial infections. Our clinical observations under an ultraviolet-induced fluorescent dermatoscope (UVFD) showed red fluorescence on the scalps of androgenetic alopecia (AGA) patients. In this study, based on the hypothesis that microbes are induced to emit red fluorescence under UV light, we aimed to explore the microbial disparities between the AGA fluorescent area (AF group) and AGA non-fluorescent area (ANF group).
METHODS
Scalp swab samples were collected from 36 AGA patients, including both fluorescent and non-fluorescent areas. The bacterial communities on the scalp were analyzed by 16S rRNA gene sequencing and bioinformatics analysis, as well as through microbial culture methods.
RESULTS
Significant variations were observed in microbial evenness, abundance composition, and functional predictions between fluorescent and non-fluorescent areas. Sequencing results highlighted significant differences in Cutibacterium abundance between these areas (34.06% and 21.36%, respectively; p < 0.05). Furthermore, cultured red fluorescent colonies primarily consisted of Cutibacterium spp., Cutibacterium acnes, Staphylococcus epidermidis, and Micrococcus spp.
CONCLUSIONS
This is the first study to investigate scalp red fluorescence, highlighting microbial composition variability across different scalp regions. These findings may provide novel insights into the microbiological mechanisms of AGA.
Topics: Humans; Alopecia; Ultraviolet Rays; Male; Adult; Middle Aged; Scalp; Female; Dermoscopy; Fluorescence; Microbiota; RNA, Ribosomal, 16S; Bacteria
PubMed: 38899718
DOI: 10.1111/srt.13777 -
Gut Microbes 2024Gut bacteria are known to produce bacteriocins to inhibit the growth of other bacteria. Consequently, bacteriocins have attracted increased attention as potential...
Gut bacteria are known to produce bacteriocins to inhibit the growth of other bacteria. Consequently, bacteriocins have attracted increased attention as potential microbiome-editing tools. In this study we examine the inhibitory spectrum of 75 class II bacteriocins against 48 representative gut microbiota species. The bacteriocins were heterologously expressed in and evaluated and assays revealed 22 bacteriocins to inhibit at least one species and showed selective inhibition patterns against species implicated in certain disorders and diseases. Three bacteriocins were selected for assessment on mouse feces. Based on 16S rRNA sequencing of the cultivated feces we showed that the two bacteriocins: Actifencin (#13) and Bacteroidetocin A (#22) selectively inhibited the growth of and , respectively. The probiotic: Nissle 1917 was engineered to express these two bacteriocins in mice. However, the selective inhibitory patterns found in the and experiments could not be observed . Our study describes a methodology for heterologous high throughput bacteriocin expression and screening and elucidates the inhibitory patterns of class II bacteriocins on the gut microbiota.
Topics: Bacteriocins; Animals; Mice; Escherichia coli; Feces; Gastrointestinal Microbiome; Anti-Bacterial Agents; RNA, Ribosomal, 16S; Lactobacillus; Bacteria; Gene Expression
PubMed: 38899682
DOI: 10.1080/19490976.2024.2369338 -
IMeta Jun 2024We investigated soil bacterial and fungal communities, constructed co-occurrence networks, and estimated bacterial traits along a gradient of nitrogen (N) input. The...
We investigated soil bacterial and fungal communities, constructed co-occurrence networks, and estimated bacterial traits along a gradient of nitrogen (N) input. The results showed that soil bacterial co-occurrence networks complexity decreased with increasing N input. The ratio of negative to positive cohesion decreased with increasing N input, suggesting the declined competitive but strengthened cooperative interactions. However, soil fungal network complexity did not change under N enrichment. In addition, N input stimulated the copiotroph/oligotroph ratio, ribosomal RNA operon () copy number, and guanine-cytosine (GC) content of soil bacteria, shifting bacterial life history strategy toward copiotroph with increased -/-strategy ratio. Piecewise structural equation modeling results further revealed that the reduction in bacterial co-occurrence network complexity was directly regulated by the increased bacterial -/-strategy ratio, rather than reduced bacterial richness. Our study reveals the mechanisms through which microbial traits regulate interactions and shape co-occurrence networks under global changes.
PubMed: 38898994
DOI: 10.1002/imt2.194 -
Nature Communications Jun 2024Reproductive success relies on proper establishment and maintenance of biological sex. In many animals, including mammals, the primary gonad is initially ovary biased....
Reproductive success relies on proper establishment and maintenance of biological sex. In many animals, including mammals, the primary gonad is initially ovary biased. We previously showed the RNA binding protein (RNAbp), Rbpms2, is required for ovary fate in zebrafish. Here, we identified Rbpms2 targets in oocytes (Rbpms2-bound oocyte RNAs; rboRNAs). We identify Rbpms2 as a translational regulator of rboRNAs, which include testis factors and ribosome biogenesis factors. Further, genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway, specifically through the mTorc1-activating Gap activity towards Rags 2 (Gator2) component, Missing oocyte (Mios). Cumulatively, our findings indicate that early gonocytes are in a dual poised, bipotential state in which Rbpms2 acts as a binary fate-switch. Specifically, Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2-mediated checkpoint, thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis.
Topics: Animals; Zebrafish; Female; Oocytes; Zebrafish Proteins; RNA-Binding Proteins; Oogenesis; Male; Ovary; Mechanistic Target of Rapamycin Complex 1; Signal Transduction; Gene Expression Regulation, Developmental; Testis; Nutrients
PubMed: 38898112
DOI: 10.1038/s41467-024-49613-2 -
Science Advances Jun 2024In the quest for new bioactive substances, nonribosomal peptide synthetases (NRPS) provide biodiversity by synthesizing nonproteinaceous peptides with high cellular...
In the quest for new bioactive substances, nonribosomal peptide synthetases (NRPS) provide biodiversity by synthesizing nonproteinaceous peptides with high cellular activity. NRPS machinery consists of multiple modules, each catalyzing a unique series of chemical reactions. Incomplete understanding of the biophysical principles orchestrating these reaction arrays limits the exploitation of NRPSs in synthetic biology. Here, we use nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry to solve the conundrum of how intermodular recognition is coupled with loaded carrier protein specificity in the tomaymycin NRPS. We discover an adaptor domain that directly recruits the loaded carrier protein from the initiation module to the elongation module and reveal its mechanism of action. The adaptor domain of the type found here has specificity rules that could potentially be exploited in the design of engineered NRPS machinery.
Topics: Peptide Synthases; Substrate Specificity; Protein Domains; Protein Binding; Magnetic Resonance Spectroscopy
PubMed: 38896613
DOI: 10.1126/sciadv.adm9404 -
ELife Jun 2024The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis...
The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis of secretory and membrane proteins. Here, we leveraged recent advances in cryo-electron microscopy (cryo-EM) and structure prediction to derive insights into several novel configurations of the ribosome-translocon complex. We show how a transmembrane domain (TMD) in a looped configuration passes through the Sec61 lateral gate during membrane insertion; how a nascent chain can bind and constrain the conformation of ribosomal protein uL22; and how the translocon-associated protein (TRAP) complex can adjust its position during different stages of protein biogenesis. Most unexpectedly, we find that a large proportion of translocon complexes contains RAMP4 intercalated into Sec61's lateral gate, widening Sec61's central pore and contributing to its hydrophilic interior. These structures lead to mechanistic hypotheses for translocon function and highlight a remarkably plastic machinery whose conformations and composition adjust dynamically to its diverse range of substrates.
Topics: Ribosomes; Cryoelectron Microscopy; SEC Translocation Channels; Endoplasmic Reticulum; Protein Conformation; Ribosomal Proteins; Humans; Models, Molecular; Protein Transport; Membrane Proteins
PubMed: 38896445
DOI: 10.7554/eLife.95814 -
Current Microbiology Jun 2024Standing dead trees (snags) are recognized for their influence on methane (CH) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude...
Standing dead trees (snags) are recognized for their influence on methane (CH) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH fluxes were highly variable (- 0.11-0.51 mg CH m h). CH production was measured in three out of ten snags; whereas, CH consumption was measured in two out of ten snags. Potential CH production and oxidation in one core from each snag was assayed in vitro. A single core produced CH under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH g h, respectively. Four cores oxidized CH under oxic conditions, with an average rate of - 1.13 ± 0.31 ng CH g h. Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH-cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH cycling in coastal ghost forest wetlands to a shifting coastal landscape.
Topics: Methane; Forests; Microbiota; Wetlands; Bacteria; RNA, Ribosomal, 16S; Trees; Phylogeny; Oxidation-Reduction; Archaea; Aerobiosis
PubMed: 38896154
DOI: 10.1007/s00284-024-03767-w -
Frontiers in Cellular and Infection... 2024The present treatments for bronchiectasis, which is defined by pathological dilatation of the airways, are confined to symptom relief and minimizing exacerbations. The... (Review)
Review
The present treatments for bronchiectasis, which is defined by pathological dilatation of the airways, are confined to symptom relief and minimizing exacerbations. The condition is becoming more common worldwide. Since the disease's pathophysiology is not entirely well understood, developing novel treatments is critically important. The interplay of chronic infection, inflammation, and compromised mucociliary clearance, which results in structural alterations and the emergence of new infection, is most likely responsible for the progression of bronchiectasis. Other than treating bronchiectasis caused by cystic fibrosis, there are no approved treatments. Understanding the involvement of the microbiome in this disease is crucial, the microbiome is defined as the collective genetic material of all bacteria in an environment. In clinical practice, bacteria in the lungs have been studied using cultures; however, in recent years, researchers use next-generation sequencing methods, such as 16S rRNA sequencing. Although the microbiome in bronchiectasis has not been entirely investigated, what is known about it suggests that , and dominate the lung bacterial ecosystems, they present significant intraindividual stability and interindividual heterogeneity. and -dominated microbiomes have been linked to more severe diseases and frequent exacerbations, however additional research is required to fully comprehend the role of microbiome in the evolution of bronchiectasis. This review discusses recent findings on the lung microbiota and its association with bronchiectasis.
Topics: Bronchiectasis; Humans; Microbiota; Lung; Bacteria; RNA, Ribosomal, 16S
PubMed: 38895737
DOI: 10.3389/fcimb.2024.1405399