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Foods (Basel, Switzerland) Oct 2022Epiphytic microbial communities significantly impact the health and quality of grape berries. This study utilized high-performance liquid chromatography and...
Epiphytic microbial communities significantly impact the health and quality of grape berries. This study utilized high-performance liquid chromatography and high-throughput sequencing to explore the epiphytic microbial diversity and physicochemical indicators in nine different wine grape varieties. In total, 1,056,651 high-quality bacterial 16S rDNA sequences and 1,101,314 fungal ITS reads were used for taxonomic categorization. Among the bacteria, Proteobacteria and Firmicutes were the dominant phyla, and , , , , , , and were the dominant genera. Among the fungi, Ascomycota and Basidiomycota were the dominant phyla, and , , , , and were the dominant genera. Notably, Matheran (MSL) and Riesling (RS) exhibited the highest microbial diversity among the nine grape varieties. Moreover, pronounced differences in epiphytic microorganisms in red and white grapes suggested that the grape variety significantly influences the structure of surface microbial communities. Understanding the composition of epiphytic microorganisms on the grape skin can provide a direct guide to winemaking.
PubMed: 37430923
DOI: 10.3390/foods11203174 -
BioRxiv : the Preprint Server For... Jun 2023Chronic polymicrobial infections (cPMIs) harbor complex bacterial communities with diverse metabolic capacities, leading to competitive and cooperative interactions....
Chronic polymicrobial infections (cPMIs) harbor complex bacterial communities with diverse metabolic capacities, leading to competitive and cooperative interactions. Although the microbes present in cPMIs have been established through culture-dependent and-independent methods, the key functions that drive different cPMIs and the metabolic activities of these complex communities remain unknown. To address this knowledge gap, we analyzed 102 published metatranscriptomes collected from cystic fibrosis sputum (CF) and chronic wound infections (CW) to identify key bacterial members and functions in cPMIs. Community composition analysis identified a high prevalence of pathogens, particularly and , and anaerobic members of the microbiota, including Functional profiling with HUMANn3 and SAMSA2 revealed that while functions involved in bacterial competition, oxidative stress response, and virulence were conserved across both chronic infection types, >40% of the functions were differentially expressed (padj < 0.05, fold-change >2). Higher expression of antibiotic resistance and biofilm functions were observed in CF, while tissue destructive enzymes and oxidative stress response functions were highly expressed in CW samples. Of note, strict anaerobes had negative correlations with traditional pathogens in both CW ( = -0.43) and CF ( = -0.27) samples and they significantly contributed to the expression of these functions. Additionally, we show microbial communities have unique expression patterns and distinct organisms fulfill the expression of key functions in each site, indicating the infection environment strongly influences bacterial physiology and that community structure influences function. Collectively, our findings indicate that community composition and function should guide treatment strategies for cPMIs.
PubMed: 37333206
DOI: 10.1101/2023.06.06.543868 -
Frontiers in Microbiology 2023The vaginal microbiota can be altered by uropathogenic bacteria associated with recurrent cystitis (RC), and the vaginal administration of have suggested certain...
BACKGROUND
The vaginal microbiota can be altered by uropathogenic bacteria associated with recurrent cystitis (RC), and the vaginal administration of have suggested certain effects to prevent RC. The relationship between vaginal microbiota and the development of RC has not been elucidated. We aimed to clarify the etiology of RC from vaginal microbiota and importance of vaginal .
METHODS
Vaginal samples obtained from 39 postmenopausal women were classified into four groups: healthy controls; uncomplicated cystitis; RC; and prevention (prevented RC by -containing vaginal suppositories). Principal coordinate analysis and beta-diversity analysis was used to assess 16S rRNA gene sequencing data from the vaginal microbiome.
RESULTS
Cluster analysis divided the vaginal bacterial communities among 129 vaginal samples into three clusters (A, B, and C). Fourteen of 14 (100%) samples from the RC group and 51 of 53 (96%) samples from the prevention group were in clusters B and C, while 29 of 38 (76%) samples from the healthy group and 14 of 24 (58%) samples from the uncomplicated cystitis group were in cluster A. The principal coordinate analysis showed that plots in the uncomplicated cystitis group were similar to the healthy group, indicating a large separation between the RC group and the uncomplicated cystitis group. On beta-diversity analysis, there were significant differences between the healthy group and the uncomplicated cystitis group ( = 0.045), and between the RC group and the uncomplicated cystitis group or the healthy group ( = 0.001, = 0.001, respectively). There were no significant differences between the RC group and the prevention group ( = 0.446). The top six taxa were as follows: and . Among patients with RC, was undetectable before administration of suppositories, while the median relative abundance of was 19% during administration of suppositories ( = 0.0211), reducing the average cystitis episodes per year (6.3 vs. 2.4, = 0.0015).
CONCLUSION
The vaginal microbiota of postmenopausal women with RC is differed from healthy controls and uncomplicated cystitis in terms of lack of and relatively dominant of . Vaginal administration of -containing suppositories can prevent RC by stabilizing vaginal dysbiosis and causing a loss of pathogenic bacteria virulence.
PubMed: 37275169
DOI: 10.3389/fmicb.2023.1187479 -
Metagenome Investigation of Ocular Microbiota of Cataract Patients With and Without Type 2 Diabetes.Translational Vision Science &... Jun 2023Our objective was to investigate differences in the ocular surface bacterial composition in cataract patients with and without type 2 diabetes (T2D).
PURPOSE
Our objective was to investigate differences in the ocular surface bacterial composition in cataract patients with and without type 2 diabetes (T2D).
METHODS
Twenty-four diabetic patients with cataracts (group D) and 14 sex- and age-matched patients with age-related cataracts (group N) were recruited for this study. All samples underwent DNA extraction, fragmentation, purification, library construction, and metagenomic sequencing.
RESULTS
The overall conjunctival sac bacterial composition was similar between group D and group N, as determined by alpha diversity and beta diversity. Nevertheless, significant differences were observed in the relative abundance of specific bacteria. At the phylum level, group D had a significantly lower abundance of Chlamydiae, Tenericutes, Chloroflexi, Cyanobacteria, Cossaviricota, Chytridiomycota, Artverviricota, Zoopagomycota, Peploviricota, Deinococcus-Thermus, Preplasmiviricota, and Nucleocytoviricota. At the genus level, group D had a significantly lower abundance of Chlamydia, Mycoplasma, Salmonella, Chryseobacterium, Roseovarius, Desulfococcus, Kangiella, Anaerococcus, and Idiomarina but a significantly higher abundance of Parabacteroides, Phocaeicola, and Sphingomonas. Bacteria such as Aquificae, Parabacteroides, Flavobacterium, Austwickia, Aquifex, Tenacibaculum, and Chryseobacterium in group D and Tenericutes, Chlamydiae, Porphyromonas, Mycoplasma, Chlamydia, Kangiella, Idiomarina, Roseovarius, Aliiroseovarius, and Desulfococcus in group N could be used as conjunctival sac biomarkers, according to the linear discriminant analysis effect size. Gene Ontology functional annotation indicated that bacterial catalytic activity, metabolic processes, locomotion, virion, and reproduction were enriched in group D, while immune system processes were enriched in group N. In addition, the top 30 differentially expressed virulence factors (VFs) were all more enriched in group D.
CONCLUSIONS
The bacterial composition was similar between the two groups. Several bacterial strains that were reported beneficial in gut were decreased, and pathogenic bacteria were increased in T2D. Furthermore, group D had more active bacterial terms and increased VF expression, suggesting that the susceptibility of diabetic patients to infection is closely related to functional changes in the ocular surface flora. Our conjunctival microbiota atlas provides a reference for investigating ocular complications related to diabetes.
TRANSLATIONAL RELEVANCE
The altered composition and functional profile of the ocular microbial community in diabetic patients offer evidence for the need to prevent infection during cataract surgery.
Topics: Humans; Bacteria; Cataract; Conjunctiva; Diabetes Mellitus, Type 2; Metagenome; Microbiota; Male; Female
PubMed: 37261381
DOI: 10.1167/tvst.12.6.1 -
Frontiers in Cellular and Infection... 2023Although recent studies have shown that the human microbiome is involved in the pathogenesis of allergic diseases, the impact of microbiota on allergic rhinitis (AR) and...
INTRODUCTION
Although recent studies have shown that the human microbiome is involved in the pathogenesis of allergic diseases, the impact of microbiota on allergic rhinitis (AR) and non-allergic rhinitis (nAR) has not been elucidated. The aim of this study was to investigate the differences in the composition of the nasal flora in patients with AR and nAR and their role in the pathogenesis.
METHOD
From February to September 2022, 35 AR patients and 35 nAR patients admitted to Harbin Medical University's Second Affiliated Hospital, as well as 20 healthy subjects who underwent physical examination during the same period, were subjected to 16SrDNA and metagenomic sequencing of nasal flora.
RESULTS
The microbiota composition of the three groups of study subjects differs significantly. The relative abundance of Vibrio vulnificus and Acinetobacter baumanni in the nasal cavity of AR patients was significantly higher when compared to nAR patients, while the relative abundance of Lactobacillus murinus, Lactobacillus iners, Proteobacteria, Pseudomonadales, and Escherichia coli was lower. In addition, Lactobacillus murinus and Lacttobacillus kunkeei were also negatively correlated with IgE, while Lacttobacillus kunkeei was positively correlated with age. The relative distribution of Faecalibacterium was higher in moderate than in severe AR patients. According to KEGG functional enrichment annotation, ICMT(protein-S-isoprenylcysteine O-methyltransferase,ICMT) is an AR microbiota-specific enzyme that plays a role, while glycan biosynthesis and metabolism are more active in AR microbiota. For AR, the model containing Parabacteroides goldstemii, Sutterella-SP-6FBBBBH3, Pseudoalteromonas luteoviolacea, Lachnospiraceae bacterium-615, and Bacteroides coprocola had the highest the area under the curve (AUC), which was 0.9733(95%CI:0.926-1.000) in the constructed random forest prediction model. The largest AUC for nAR is 0.984(95%CI:0.949-1.000) for the model containing Pseudomonas-SP-LTJR-52, Lachnospiraceae bacterium-615, Prevotella corporis, Anaerococcus vaginalis, and Roseburia inulinivorans.
CONCLUSION
In conclusion, patients with AR and nAR had significantly different microbiota profiles compared to healthy controls. The results suggest that the nasal microbiota may play a key role in the pathogenesis and symptoms of AR and nAR, providing us with new ideas for the treatment of AR and nAR.
Topics: Humans; Male; Female; Young Adult; Adult; Rhinitis, Allergic; Rhinitis; Nasal Cavity; Metagenome; Biodiversity; Microbiota; RNA, Ribosomal, 16S; Bacteria
PubMed: 37180436
DOI: 10.3389/fcimb.2023.1166389 -
International Journal of Molecular... Apr 2023Since the first description of a commensal seminal microbiome using sequencing, less than a decade ago, interest in the composition of this microbiome and its...
Since the first description of a commensal seminal microbiome using sequencing, less than a decade ago, interest in the composition of this microbiome and its relationship with fertility has been growing. Articles using next-generation sequencing techniques agree on the identification of the most abundant bacterial phyla. However, at the genus level, there is still no consensus on which bacteria are most abundant in human seminal plasma. This discrepancy may be due to methodological variability such as sample collection, bacterial DNA extraction methodology, which hypervariable regions of gene have been amplified, or bioinformatic analysis. In the present work, seminal microbiota of 14 control samples and 42 samples of idiopathic infertile patients were characterized based on full-length sequencing of the gene using MinION platform from Oxford Nanopore. These same samples had been analyzed previously using Illumina's MiSeq sequencing platform. Comparison between the results obtained with the two platforms has been used to analyze the impact of sequencing method on the study of the seminal microbiome's composition. Seminal microbiota observed with MinION were mainly composed of the phyla , , and , with the most abundant genera being , , , , , , , , and . This composition was similar to that found by the Illumina platform, since these 10 most abundant genera were also among the most abundant genera detected by the Nanopore platform. In both cases, the top 10 genera represented more than 70% of the classified reads. However, relative abundance of each bacterium did not correlate between these two platforms, with intraindividual variations of up to 50 percentage points in some cases. Results suggest that the effect of the sequencing platform on the characterization of seminal microbiota is not very large at the phylum level, with slightly variances in and , but presents differences at the genus level. These differences could alter the composition and diversity of bacterial profiles or posterior analyses. This indicates the importance of conducting multi-platform studies to better characterize seminal microbioma.
Topics: Humans; RNA, Ribosomal, 16S; Microbiota; Bacteria; Firmicutes; Proteobacteria; Actinobacteria; High-Throughput Nucleotide Sequencing; Clostridiales
PubMed: 37175573
DOI: 10.3390/ijms24097867 -
Microorganisms Mar 2023Although high-risk human papillomavirus infection is a well-established risk factor for cervical cancer, other co-factors within the local microenvironment may play an...
Although high-risk human papillomavirus infection is a well-established risk factor for cervical cancer, other co-factors within the local microenvironment may play an important role in the development of cervical cancer. The current study aimed to characterize the cervicovaginal microbiota in women with premalignant dysplasia or invasive cervical cancer compared with that of healthy women. The study comprised 120 Ethiopian women (60 cervical cancer patients who had not received any treatment, 25 patients with premalignant dysplasia, and 35 healthy women). Cervicovaginal specimens were collected using either an Isohelix DNA buccal swab or an Evalyn brush, and ribosomal RNA sequencing was used to characterize the cervicovaginal microbiota. Shannon and Simpson diversity indices were used to evaluate alpha diversity. Beta diversity was examined using principal coordinate analysis of weighted UniFrac distances. Alpha diversity was significantly higher in patients with cervical cancer than in patients with dysplasia and in healthy women ( < 0.01). Beta diversity was also significantly different in cervical cancer patients compared with the other groups (weighted UniFrac Bray-Curtis, < 0.01). Microbiota composition differed between the dysplasia and cervical cancer groups. was particularly enriched in patients with cancer, and a high relative abundance of species was identified in the dysplasia and healthy groups, whereas , , , and species predominated in the cervical cancer group. In summary, we identified differences in cervicovaginal microbiota diversity, composition, and relative abundance between women with cervical cancer, women with dysplasia, and healthy women. Additional studies need to be carried out in Ethiopia and other regions to control for variation in sample collection.
PubMed: 37110255
DOI: 10.3390/microorganisms11040833 -
Frontiers in Immunology 2023Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects gut luminal cells through the angiotensin-converting enzyme-2 receptor and disrupts the gut...
OBJECTIVES
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects gut luminal cells through the angiotensin-converting enzyme-2 receptor and disrupts the gut microbiome. We investigated whether the gut microbiome in the early stage of SARS-CoV-2 infection was associated with the prognosis of coronavirus disease (COVID-19).
METHODS
Thirty COVID-19 patients and 16 healthy controls were prospectively enrolled. Blood and stool samples and clinical details were collected on days 0 (enrollment), 7, 14, and 28. Participants were categorized into four groups by their clinical course.
RESULTS
Gut microbiota composition varied during the clinical course of COVID-19 and was closely associated with cytokine levels (=0.003). A high abundance of the genus (linear discriminant analysis [LDA] effect size: 3.97856, =0.004), species (LDA effect size: 4.00551, =0.020), and (LDA effect size: 4.00885, =0.007) was associated with a good prognosis. Starch, sucrose, and galactose metabolism was highly activated in the gut microbiota of the poor prognosis group. Glucose-lowering diets, including whole grains, were positively correlated with a good prognosis.
CONCLUSION
Gut microbiota may mediate the prognosis of COVID-19 by regulating cytokine responses and controlling glucose metabolism, which is implicated in the host immune response to SARS-CoV-2.
Topics: Humans; COVID-19; Gastrointestinal Microbiome; SARS-CoV-2; Cytokines; Prognosis; Disease Progression
PubMed: 37051240
DOI: 10.3389/fimmu.2023.1079277 -
Microorganisms Mar 2023In ruminant livestock production, ruminal acidosis is an unintended consequence of the elevated dietary intake of starch-rich feedstuffs. The transition from a state of...
In ruminant livestock production, ruminal acidosis is an unintended consequence of the elevated dietary intake of starch-rich feedstuffs. The transition from a state of subacute acidosis (SARA) to acute acidosis is due in large part to the accumulation of lactate in the rumen, which is a consequence of the inability of lactate utilizers to compensate for the increased production of lactate. In this report, we present the 16S rRNA gene-based identification of two bacterial operational taxonomic units (OTUs), Bt-01708_Bf (89.0% identical to ) and Bt-01899_Ap (95.3% identical to ), that were enriched from rumen fluid cultures in which only lactate was provided as an exogenous substrate. Analyses of in-silico-predicted proteomes from metagenomics-assembled contigs assigned to these candidate ruminal bacterial species (Bt-01708_Bf: 1270 annotated coding sequences, 1365 hypothetical coding sequences; Bt-01899_Ap: 871 annotated coding sequences, 1343 hypothetical coding sequences) revealed genes encoding lactate dehydrogenase, a putative lactate transporter, as well as pathways for the production of short chain fatty acids (formate, acetate and butyrate) and for the synthesis of glycogen. In contrast to these shared functions, each OTU also exhibited distinct features, such as the potential for the utilization of a diversified set of small molecules as substrates (Bt-01708_Bf: malate, quinate, taurine and polyamines) or for the utilization of starch (Bt-01899_Ap: alpha-amylase enzymes). Together, these results will contribute to the continued characterization of ruminal bacterial species that can metabolize lactate into distinct subgroups based on other metabolic capabilities.
PubMed: 36985231
DOI: 10.3390/microorganisms11030658 -
Antibiotics (Basel, Switzerland) Mar 2023The SARS-CoV-2 infection has increased the number of patients entering Intensive Care Unit (ICU) facilities and antibiotic treatments. Concurrently, the multi-drug...
The SARS-CoV-2 infection has increased the number of patients entering Intensive Care Unit (ICU) facilities and antibiotic treatments. Concurrently, the multi-drug resistant bacteria (MDRB) colonization index has risen. Considering that most of these bacteria are derived from gut microbiota, the study of its composition is essential. Additionally, SARS-CoV-2 infection may promote gut dysbiosis, suggesting an effect on microbiota composition. This pilot study aims to determine bacteria biomarkers to predict MDRB colonization risk in SARS-CoV-2 patients in ICUs. Seventeen adult patients with an ICU stay >48 h and who tested positive for SARS-CoV-2 infection were enrolled in this study. Patients were assigned to two groups according to routine MDRB colonization surveillance: non-colonized and colonized. Stool samples were collected when entering ICUs, and microbiota composition was determined through Next Generation Sequencing techniques. Gut microbiota from colonized patients presented significantly lower bacterial diversity compared with non-colonized patients ( < 0.05). Microbiota in colonized subjects showed higher abundance of , and , while higher levels of , and were found in non-colonized ones. Moreover, LEfSe analysis suggests an initial detection of as a biomarker of MDRB colonization risk. This pilot study shows that gut microbiota profile can become a predictor biomarker for MDRB colonization in SARS-CoV-2 patients.
PubMed: 36978365
DOI: 10.3390/antibiotics12030498