The oral microbiome of newly diagnosed tuberculosis patients; a pilot study.

BACKGROUND: Changes in oral microbiota composition (dysbiosis) have long been known to play a key role in the pathogenesis of oral and systemic diseases including respiratory diseases. However, till now, no study has assessed changes in oral microbiota following tuberculosis (TB) infection in humans. AIMS: This is the first study of its kind that aimed to investigate oral microbial dysbiosis in newly diagnosed, treatment naïve, TB patients. METHODS: Oral swab samples were collected from newly diagnosed TB patients (n = 20) and age, gender and ethnicity matched healthy controls (n = 10). DNA was extracted and microbiota analyzed by sequencing the hypervariable (V3-V4) region of the bacterial 16S rRNA gene using Illumina MiSeq platform. Bioinformatics and statistical analyses were performed using QIIME and R. RESULTS: Bacterial richness, diversity and community composition were significantly different between TB patients and healthy controls. The two groups also exhibit differential abundance at phylum, class, genus and species levels. LEfSe analysis revealed enrichment (LDA scores (log10) >2, P < 0.05) of Firmicutes (especially Streptococcus) and Actinobacteriota (especially Rothia) in TB patients relative to healthy controls. Gene function prediction analysis showed upregulation of metabolic pathways related to carbohydrates (butanoate, galactose) and fatty acids metabolism, antibiotics biosynthesis, proteosome and immune system signaling. CONCLUSION: These observations suggest significant variations in diversity, relative abundance and functional potential of oral microbiota of TB patients compared to healthy controls thereby suggesting potential role of oral bacterial dysbiosis in TB pathogenesis. However, longitudinal studies using powerful metagenomic and transcriptomic approaches are crucial to more fully understand and confrim these findings.

Human uridine 5'-monophosphate synthase stores metabolic potential in inactive biomolecular condensates.

Human uridine 5'-monophosphate synthase (HsUMPS) is a bifunctional enzyme that catalyzes the final two steps in de novo pyrimidine biosynthesis. The individual orotate phosphoribosyl transferase and orotidine monophosphate domains have been well characterized, but little is known about the overall structure of the protein and how the organization of domains impacts function. Using a combination of chromatography, electron microscopy, and complementary biophysical methods, we report herein that HsUMPS can be observed in two structurally distinct states, an enzymatically active dimeric form and a nonactive multimeric form. These two states readily interconvert to reach an equilibrium that is sensitive to perturbations of the active site and the presence of substrate. We determined that the smaller molecular weight form of HsUMPS is an S-shaped dimer that can self-assemble into relatively well-ordered globular condensates. Our analysis suggests that the transition between dimer and multimer is driven primarily by oligomerization of the orotate phosphoribosyl transferase domain. While the cellular distribution of HsUMPS is unaffected, quantification by mass spectrometry revealed that de novo pyrimidine biosynthesis is dysregulated when this protein is unable to assemble into inactive condensates. Taken together, our data suggest that HsUMPS self-assembles into biomolecular condensates as a means to store metabolic potential for the regulation of metabolic rates.

Gimibacter soli gen. nov. sp. nov., isolated from mangrove soil and insight into its ecological distribution and metabolic potential.

A Gram-stain-negative, facultatively anaerobic, motile and rod-shaped bacterium, designated as 6D33T, was isolated from mangrove soil. Growth was found to occur at 15-32 °C (optimum, 28 °C), at pH 6-9 (optimum, pH 7) and in 0-3 % NaCl (optimum, 1 %, w/v). The results of 16S rRNA gene-based analysis showed that strain 6D33T belonged to the family Temperatibacteraceae, sharing 93.1-94.4 % identity with its close neighbours within the genus Kordiimonas. The phylogenomic results indicated that strain 6D33T formed an independent branch distinct from type strains of the genus Kordiimonas. The overall genome relatedness indices of digital DNA-DNA hybridization, average nucleotide identity and amino acid identity values showed that strain 6D33T represents a novel species of a novel genus. The results of chemotaxonomic characterization indicated that the major cellular fatty acids of strain 6D33T were summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1 ω9c), summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and iso-C15 : 0; the polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and three unidentified lipids; the only respiratory quinone was ubiquinone-10. The genomic size and DNA G+C contents were 3.59 Mbp and 60.84 mol%, respectively. The 16S rRNA gene sequence reads abundance profiles revealed that the rare taxon is prevalent in marine environments, especially in sediments. Genome-scale metabolic reconstruction of strain 6D33T revealed a heterotrophic lifestyle and many pathways responsible for the degradation of aromatic compounds, suggesting application potential in aromatic hydrocarbon removal. Based on its genotypic and phenotypic characteristics, strain 6D33T is concluded to represent a novel species of the novel genus in the family Temperatibacteraceae, for which the name Gimibacter soli gen. nov. sp. nov. is proposed. The type strain of the type species is 6D33T (=GDMCC 1.1959T=KCTC 82335T).

Metatranscriptomic insight into the possible role of clay microbiome in skin disease management.

Even though the scientific documentation is limited, microbiome of healing clay is gradually gaining attention of the scientific community, as a therapeutic force playing an indispensable role in skin disease management. The present study explores the metatranscriptome profile of the Chamliyal clay, widely known for its efficacy in managing various skin problems, using Illumina NextSeq sequencing technology. The gene expression profile of the clay microbial community was analyzed through SEED subsystems of the MG-RAST server. Due to the unavailability of metatranscriptomic data on other therapeutic clays, Chamliyal's profile was compared to non-therapeutic soils, as well as healthy and diseased human skin microbiomes. The study identified Firmicutes, Proteobacteria, and Actinobacteria as the primary active microbial phyla in Chamliyal clay. These resemble those abundant in a healthy human skin microbiome. This is significant as lower levels of these phyla in the skin are linked to inflammatory skin conditions like psoriasis. Interestingly, pathogenic microbes actively metabolizing in the clay were absent. Importantly, 6% of the transcripts annotated to sulfur and iron metabolism, which are known to play a major role in skin disease management. This study provides the most comprehensive and a novel overview of the metatranscriptome of any of the healing clay available worldwide. The findings offer valuable insights into the clay microbiome's potential in managing skin disorders, inspiring future endeavors to harness these insights for medical applications.

Deep-sea sediment metagenome from Bay of Bengal reveals distinct microbial diversity and functional significance.

Bay of Bengal (BoB) has immense significance with respect to ecological diversity and natural resources. Studies on microbial profiling and their functional significance at sediment level of BoB remain poorly represented. Herein, we describe the microbial diversity and metabolic potentials of BOB deep-sea sediment samples by subjecting the metagenomes to Nanopore sequencing. Taxonomic diversity ascertained at various levels revealed that bacteria belonging to phylum Proteobacteria predominantly represented in sediment samples NIOT_S7 and NIOT_S9. A comparative study with 16S datasets from similar ecological sites revealed depth as a crucial factor in determining taxonomic diversity. KEGG annotation indicated that bacterial communities possess sequence reads corresponding to carbon dioxide fixation, sulfur, nitrogen metabolism, but at varying levels. Additionally, gene sequences related to bioremediation of dyes, plastics, hydrocarbon, antibiotic resistance, secondary metabolite synthesis and metal resistance from both the samples as studied indicate BoB to represent a highly diverse environmental niche for further exploration.

Pollutants removal and connections among sludge properties, metabolism potential and microbial characteristics in aerobic granular sequencing batch reactor for petrochemical wastewater treatment.

Petrochemical wastewater contains inhibitory compounds such as aromatics that are toxic to microorganisms during biological treatment. The compact and layered structure and the high amount of extracellular polymeric substances (EPS) in aerobic granular sludge (AGS) can contribute to protecting microorganisms from the harsh environment. This study evaluated the changes in the granule properties, pollutants removal, microbial metabolic potential and molecular microbial characteristics of the AGS process for petrochemical wastewater treatment. Granules treating petrochemical wastewater had a higher SVI30/SVI5 value (0.94) than that treating synthetic wastewater. An increase in bioactivity and EPS secretion with higher bio-polymer composition, specifically the functional groups such as hydroxyl, alkoxy and amino in protein, was observed, which promoted biomass aggregation. The granules also had more than 2-fold higher specific oxygen utilization rate. The AGS-SBR process obtained an average COD removal of 93% during petrochemical wastewater treatment and an effluent bCOD of below 1 mg L-1. No obvious inhibition of nitrification and denitrification activity was observed in the processes attributed to the layered structure of AGS. The average effluent NH4+-N of 5.0 mg L-1 was obtained and TN removal efficiencies of over 80.0% was achieved. Molecular microbial analysis showed that abundant functional genera Stenotrophomonas and Pseudoxanthomonas contributed to the degradation of aromatics and other petroleum organic pollutants. They were enriched with the variation of group behavior while metabolisms of amino acids and carboxylic acids by the relevant functional genera (e.g., Cytophagia) were significantly inhibited. The enrichment of Flavobacterium and Thermomonas promoted nitrification and denitrification, respectively. This research revealed the rapid start-up, enhanced granule structural strength, high inhibition resistance and considerable performance of AGS-SBR for petrochemical wastewater treatment.

Microbial Enrichment Techniques on Syngas and CO2 Targeting Production of Higher Acids and Alcohols.

(1) Background: Microbial conversion of gaseous molecules, such as CO2, CO and H2, to valuable compounds, has come to the forefront since the beginning of the 21st century due to increasing environmental concerns and the necessity to develop alternative technologies that contribute to a fast transition to a more sustainable era. Research efforts so far have focused on C1-C2 molecules, i.e., ethanol and methane, while interest in molecules with higher carbon atoms has also started to emerge. Research efforts have already started to pay off, and industrial installments on ethanol production from steel-mill off-gases as well as methane production from the CO2 generated in biogas plants are a reality. (2) Methodology: The present study addresses C4-C6 acids and butanol as target molecules and responds to how the inherent metabolic potential of mixed microbial consortia could be revealed and exploited based on the application of different enrichment methods (3) Results and Conclusions: In most of the enrichment series, the yield of C4-C6 acids was enhanced with supplementation of acetic acid and ethanol together with the gas substrates, resulting in a maximum of 43 and 68% (e-mol basis) for butyric and caproic acid, respectively. Butanol formation was also enhanced, to a lesser degree though and up to 9% (e-mol basis). Furthermore, the microbial community exhibited significant shifts depending on the enrichment conditions applied, implying that a more profound microbial analysis on the species level taxonomy combined with the development of minimal co-cultures could set the basis for discovering new microbial co-cultures and/or co-culturing schemes.

Metabolic Potential of the Gut Microbiome Is Significantly Impacted by Conditioning Regimen in Allogeneic Hematopoietic Stem Cell Transplantation Recipients.

Allogeneic hematopoietic stem cell transplantation (aHSCT) is a putative curative treatment for malignant hematologic disorders. During transplantation, the immune system is suppressed/eradicated through a conditioning regimen (non-myeloablative or myeloablative) and replaced with a donor immune system. In our previous study, we showed changes in gut taxonomic profiles and a decrease in bacterial diversity post-transplant. In this study, we expand the cohort with 114 patients and focus on the impact of the conditioning regimens on taxonomic features and the metabolic functions of the gut bacteria. This is, to our knowledge, the first study to examine the metabolic potential of the gut microbiome in this patient group. Adult aHSCT recipients with shotgun sequenced stool samples collected day -30 to +28 relative to aHSCT were included. One sample was selected per patient per period: pre-aHSCT (day -30-0) and post-aHSCT (day 1-28). In total, 254 patients and 365 samples were included. Species richness, alpha diversity, gene richness and metabolic richness were all lower post-aHSCT than pre-aHSCT and the decline was more pronounced for the myeloablative group. The myeloablative group showed a decline in 36 genera and an increase in 15 genera. For the non-myeloablative group, 30 genera decreased and 16 increased with lower fold changes than observed in the myeloablative group. For the myeloablative group, 32 bacterial metabolic functions decreased, and one function increased. For the non-myeloablative group, three functions decreased, and two functions increased. Hence, the changes in taxonomy post-aHSCT caused a profound decline in bacterial metabolic functions especially in the myeloablative group, thus providing new evidence for associations of myeloablative conditioning and gut dysbiosis from a functional perspective.

Differences in Gut Microbiota Composition and Predicted Metabolic Functions: a Pilot Study of Adolescents with Normal Weight and Obesity.

Understanding the principles underlying the stability and sustainability of the gut microbiome of adolescents with normal weight and obesity will make it possible to implement a personalized approach to the correction of metabolic disorders. The article presents the results of a pilot study of the diversity and metabolic potential of the gut microbiome in adolescents with normal body weight and obesity. Biological material was studied using metagenomic sequencing of the V3-V4 variable regions of the 16S rRNA gene. In all adolescents with normal weight, similar degree of the phylogenetic relationship between the bacterial taxa of the community was demonstrated. In contrast, obese adolescents were characterized by the presence of phylogenetically distinct taxa in the gut microbiota. However, even with differences in taxonomic composition, the gut microbial community can compensate for the absence of certain taxonomic groups by implementing the necessary metabolic functions using other phylogenetically close taxa.

MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes.

BACKGROUND: High-throughput sequencing has increased the number of available microbial genomes recovered from isolates, single cells, and metagenomes. Accordingly, fast and comprehensive functional gene annotation pipelines are needed to analyze and compare these genomes. Although several approaches exist for genome annotation, these are typically not designed for easy incorporation into analysis pipelines, do not combine results from different annotation databases or offer easy-to-use summaries of metabolic reconstructions, and typically require large amounts of computing power for high-throughput analysis not available to the average user. RESULTS: Here, we introduce MicrobeAnnotator, a fully automated, easy-to-use pipeline for the comprehensive functional annotation of microbial genomes that combines results from several reference protein databases and returns the matching annotations together with key metadata such as the interlinked identifiers of matching reference proteins from multiple databases [KEGG Orthology (KO), Enzyme Commission (E.C.), Gene Ontology (GO), Pfam, and InterPro]. Further, the functional annotations are summarized into Kyoto Encyclopedia of Genes and Genomes (KEGG) modules as part of a graphical output (heatmap) that allows the user to quickly detect differences among (multiple) query genomes and cluster the genomes based on their metabolic similarity. MicrobeAnnotator is implemented in Python 3 and is freely available under an open-source Artistic License 2.0 from https://github.com/cruizperez/MicrobeAnnotator . CONCLUSIONS: We demonstrated the capabilities of MicrobeAnnotator by annotating 100 Escherichia coli and 78 environmental Candidate Phyla Radiation (CPR) bacterial genomes and comparing the results to those of other popular tools. We showed that the use of multiple annotation databases allows MicrobeAnnotator to recover more annotations per genome compared to faster tools that use reduced databases and is computationally efficient for use in personal computers. The output of MicrobeAnnotator can be easily incorporated into other analysis pipelines while the results of other annotation tools can be seemingly incorporated into MicrobeAnnotator to generate summary plots.