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Biotechnology For Biofuels 2018The production of 1 L of ethanol from sugarcane generates up to 12 L of vinasse, which is a liquid waste containing an as-yet uncharacterized microbial assemblage....
BACKGROUND
The production of 1 L of ethanol from sugarcane generates up to 12 L of vinasse, which is a liquid waste containing an as-yet uncharacterized microbial assemblage. Most vinasse is destined for use as a fertilizer on the sugarcane fields because of the high organic and K content; however, increased NO emissions have been observed when vinasse is co-applied with inorganic N fertilizers. Here we aimed to characterize the microbial assemblage of vinasse to determine the gene potential of vinasse microbes for contributing to negative environmental effects during fertirrigation and/or to the obstruction of bioethanol fermentation.
RESULTS
We measured chemical characteristics and extracted total DNA from six vinasse batches taken over 1.5 years from a bioethanol and sugar mill in Sao Paulo State. The vinasse microbial assemblage was characterized by low alpha diversity with 5-15 species across the six vinasses. The core genus was . The top six represented bacterial genera across the samples were , and (Phylum Firmicutes, 35-97% of sample reads); and (Phylum Proteobacteria, 0-40%); (Phylum Bacteroidetes, 0-53%); and (Phylum Actinobacteria, 0-18%). Potential genes for denitrification but not nitrification were identified in the vinasse metagenomes, with putative K and Z genes the most represented. Binning resulted in 38 large bins with between 36.0 and 99.3% completeness, and five small mobile element bins. Of the large bins, 53% could be classified at the phylum level as Firmicutes, 15% as Proteobacteria, 13% as unknown phyla, 13% as Bacteroidetes and 6% as Actinobacteria. The large bins spanned a range of potential denitrifiers; moreover, the genetic repertoires of all the large bins included the presence of genes involved in acetate, CO, ethanol, HO, and lactose metabolism; for many of the large bins, genes related to the metabolism of mannitol, xylose, butyric acid, cellulose, sucrose, "3-hydroxy" fatty acids and antibiotic resistance were present based on the annotations. In total, 21 vinasse bacterial draft genomes were submitted to the genome repository.
CONCLUSIONS
Identification of the gene repertoires of vinasse bacteria and assemblages supported the idea that organic carbon and nitrogen present in vinasse together with microbiological variation of vinasse might lead to varying patterns of NO emissions during fertirrigation. Furthermore, we uncovered draft genomes of novel strains of known bioethanol contaminants, as well as draft genomes unknown at the phylum level. This study will aid efforts to improve bioethanol production efficiency and sugarcane agriculture sustainability.
PubMed: 29483941
DOI: 10.1186/s13068-018-1036-9 -
Frontiers in Cellular and Infection... 2021Vaginal dysbiosis, such as bacterial vaginosis (BV) and aerobic vaginitis (AV), is an important cause of premature birth in pregnant women. However, there is very little...
Vaginal dysbiosis, such as bacterial vaginosis (BV) and aerobic vaginitis (AV), is an important cause of premature birth in pregnant women. However, there is very little research on vaginal microbial distribution in AV compared to that in BV. This study aimed to analyze the composition of the vaginal microbiota of pregnant women with AV using microbial community analysis and identify the causative organism using each criterion of the AV scoring system. Also, we compared the quantification of aerobic bacteria using quantitative polymerase chain reaction (qPCR) and their relative abundances (RA) using metagenomics. This prospective case-control study included 228 pregnant Korean women from our previous study. A wet mount test was conducted on 159 women to diagnose AV using the AV scoring system. Vaginal samples were analyzed using metagenomics, Gram staining for Nugent score determination, conventional culture, and qPCR for spp. spp., and . The relative abundances (RAs) of eleven species showed significant differences among the three groups (Normal flora (NF), mild AV, and moderate AV). Three species including were significantly lower in the AV groups than in the NF group, while eight species were higher in the AV groups, particularly moderate AV. The decrease in the RA of was common in three criteria of the AV scoring system (, WBC, and background flora grades), while it did not show a significant difference among the three grade groups of the toxic leukocyte criterion. Also, the RAs of anaerobes, such as and , were higher in the AV groups, particularly moderate AV, while the RAs of aerobes were very low (RA < 0.01). Therefore, qPCR was performed for aerobes ( spp. spp., and ); however, their quantification did not show a higher level in the AV groups when compared to that in the NF group. Therefore, AV might be affected by the RA of spp. and the main anaerobes, such as spp. Activation of leukocytes under specific conditions might convert them to toxic leukocytes, despite high levels of . Thus, the pathogenesis of AV can be evaluated under such conditions.
Topics: Case-Control Studies; Dysbiosis; Female; Humans; Microbiota; Pregnancy; Pregnant Women; Vagina; Vaginitis
PubMed: 34568084
DOI: 10.3389/fcimb.2021.677648 -
Sexual Medicine Aug 2023The loop electrosurgical excision procedure (LEEP) to treat cervical dysplasia (CD) is known to alter the cervical microbiota, the community of bacteria that play a...
BACKGROUND
The loop electrosurgical excision procedure (LEEP) to treat cervical dysplasia (CD) is known to alter the cervical microbiota, the community of bacteria that play a central role in female genital health. Perturbations to the microbiota of the female urogenital tract (FUT), including the urethra, vagina, and cervix, have been linked with symptoms of sexual dysfunction (SD), though correlations among LEEP, the microenvironment, and SD have not yet been described.
AIMS
To characterize the FUT microbiota before and after LEEP and investigate possible associations with SD.
METHODS
Females undergoing LEEP for CD were recruited to participate in the study. Urinary samples and vaginal and cervical swabs were collected immediately before and 3 months after treatment. Bacterial communities were characterized by 16S rRNA next-generation sequencing. Self-report surveys assessing demographics, medical history, and sexual function were completed at the same intervals.
OUTCOMES
Microbiota taxonomy and Female Sexual Function Index (FSFI) scores.
RESULTS
Alpha diversity revealed a significant decrease in species richness in the FUT microbiota post-LEEP. Beta diversity demonstrated significant differences among the cervical, urinary, and vaginal microenvironments pre- and post-LEEP. spp were the dominant microbial genus in the cervical microenvironment pre- and post-LEEP. Although the vaginal and urinary microenvironments were characterized by pre-LEEP, they were colonized by post-LEEP. Following LEEP, some participants experienced a significant increase in proinflammatory bacteria, including the genera , , , , and Others experienced significant decreases in inflammatory and protective bacteria post-LEEP, including , , , and Overall there were no significant changes in pre- and post-LEEP FSFI scores. However, post-LEEP FSFI scores were seemingly associated with changes in inflammatory bacteria in some participants.
CLINICAL IMPLICATIONS
There is an overall reduction in FUT microbiota dysbiosis post-LEEP. However, we show variability as some participants experienced persistent dysbiosis of FUT microbiota and elevated FSFI scores, suggesting that therapies to treat dysbiosis of FUT microbiota may reduce FSFI scores, thereby improving SD symptoms.
STRENGTHS AND LIMITATIONS
We demonstrate novel associations among urogenital sites, microbiota changes, LEEP, and SD. The small sample size and inability of species classification are limitations.
CONCLUSION
Diverse inflammatory microbiota characterizes CD in the FUT, and LEEP mostly returns microenvironments to a healthy state. However, some participants have persistent inflammatory bacteria post-LEEP, suggesting a non-uniform healing response. This study provides an impetus for future longitudinal studies to monitor and restore FUT microenvironments post-LEEP, aimed at mitigating postoperative SD symptoms.
PubMed: 37588087
DOI: 10.1093/sexmed/qfad039 -
Research Square Aug 2023Tuberculosis (TB) infection is known to lead to the unbalance of the gut microbiota and act synergistically on the decline of the host immune response, when untreated....
BACKGROUND
Tuberculosis (TB) infection is known to lead to the unbalance of the gut microbiota and act synergistically on the decline of the host immune response, when untreated. Moreover, previous work has found a correlation between dysbiosis in the gut microbiota composition and the use of antibiotics. However, there is a need for an in-depth understanding of the metabolic and immune consequences of antibiotic-related microbiome alterations during first-line TB treatment.
METHODS
In a longitudinal cohort study, which included TB-infected cohorts and healthy individuals (control group), we studied the anti-TB-related changes in the gut microbiota composition and related functional consequences. Sputum, whole blood and stool samples were collected from participants at four time-points including before (Month-0), during (Month-2), at the end of drug treatment (Month-6) and 9 months after treatment (Month-15). Controls were sampled at inclusion and Month-6. We analyzed the microbiota composition and microbial functional pathways with shotgun metagenomics, analyzed the blood metabolomics using high-performance liquid chromatography (HPLC), and measured the levels of metabolites and cytokines with cytometric bead array.
RESULTS
We found that the gut microbiota of patients infected with TB was different from that of the healthy controls. The gut microbiota became similar to healthy controls after treatment but was still significantly different after 6 months treatment and at the follow up 9 months after treatment. Our data also showed disturbance in the plasma metabolites such as tryptophan and tricarboxylic acids components of patients during TB treatment. Levels of IL-4, IL-6, IL-10, and IFN-γ decreased during treatment and levels were maintained after treatment completion, while IL-17A known to have a strong link with the gut microbiota was highly expressed during treatment period and longer than the 9-month post treatment completion. We found that some fatty acids were negatively correlated with the abundance of taxa. For example, , and HIMB5 species were negatively correlated (rho = -0.6) with the quinolinate production.
CONCLUSION
Changes in the composition and function of gut microbiota was observed in TB patients before and after treatment compared to healthy controls. The differences persisted at nine months after treatment completion. Alterations in some bacterial taxa were correlated to the changes in metabolite levels in peripheral blood, thus the altered microbial community might lead to changes in immune status that influence the disease outcome and future resistance to infections.
PubMed: 37609282
DOI: 10.21203/rs.3.rs-3232670/v1 -
Journal of Dairy Science Dec 2023The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use...
The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use strategies for ruminal acidosis control. Rumen bacterial and archaeal community composition (BCC) and its associations with rumen fermentation measures were examined in Holstein heifers fed feed additives and challenged with starch and fructose. Heifers (n = 40) were randomly allocated to 5 treatment groups: (1) control (no additives); (2) virginiamycin (VM; 200 mg/d); (3) monensin (MT; 200 mg/d) + tylosin (110 mg/d); (4) monensin (MLY; 220 mg/d) + live yeast (5.0 × 10 cfu/d); (5) sodium bicarbonate (BUF; 200 g/d) + magnesium oxide (30 g/d). Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of body weight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d 21 heifers were challenged once with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). A rumen sample was collected from each heifer via stomach tube weekly (d 0, 7, 14) and 5 times over a 3.6 h period at 5, 65, 115, 165, and 215 min after consumption of the challenge ration (d 21) and analyzed for pH, and ammonia, d- and l-lactate, volatile fatty acids (VFA), and histamine concentrations and total bacteria and archaea. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced. Alpha and β diversity and associations of relative abundances of taxa with rumen fermentation measures were evaluated. Rumen BCC shifted among treatment groups in the adaptation period and across the challenge sampling period, indicating the feed additives had different modes of action. The monensin-containing treatment groups, MT and MLY often had similar relative abundances of rumen bacterial phyla and families. The MLY treatment group was characterized in the challenge period by increased relative abundances of the lactate utilizing genera Anaerovibrio and Megasphaera. The MLY treatment group also had increased diversity of ruminal bacteria which may provide resilience to changes in substrates. The control and BUF treatment groups were most similar in BCC. A redundancy analysis showed the MLY treatment group differed from all other treatment groups and concentrations of histamine and valerate in the rumen were associated with the most variation in the microbiota, 5.3% and 4.8%, respectively. It was evident from the taxa common to all treatment groups that cattle have a core microbiota. Functional redundancy of rumen bacteria which was reflected in the greater sensitivity for the rumen BCC than rumen fermentation measures likely provide resilience to changes in substrate. This functional redundancy of microbes in cattle suggests that there is no single optimal ruminal microbial population and no universally superior feed additive(s). In summary, differences in modes of action suggest the potential for more targeted and improved prudent use of feed additives with no single feed additive(s) providing an optimal BCC in all heifers.
Topics: Animals; Cattle; Female; Acidosis; Animal Feed; Archaea; Bacteria; Diet; Fermentation; Fructose; Histamine; Hydrogen-Ion Concentration; Lactates; Monensin; RNA, Ribosomal, 16S; Rumen; Saccharomyces cerevisiae; Starch
PubMed: 37678787
DOI: 10.3168/jds.2023-23486 -
Journal of Cancer Research and... 2022Gut microbiota plays an important role in the development of different diseases including colorectal cancer. The geography, lifestyle, and dietary habits of Indians are...
BACKGROUND
Gut microbiota plays an important role in the development of different diseases including colorectal cancer. The geography, lifestyle, and dietary habits of Indians are different from Western world, thus microbiome studies of Western population could not be extrapolated to their Indian counterparts.
METHOD
Therefore, we have conducted a study on gut microbiota in Indian healthy subjects and patients of colon cancer using 16S ribosomal RNA Amplicon sequencing. Operational taxonomic units were calculated for different bacterial taxon including phylum, class, order, family, and genus level.
RESULTS
Observed results indicated a considerable difference in the bacterial diversity in both the groups. Phylum Firmicutes was significantly dominated in both the groups followed by Bacteroidetes, Actinobacteria, and Proteobacteria which clearly indicates the dominance of phylum Firmicutes in Indian population. Phylum Firmicutes and Actinobacteria were significantly abundant in the healthy group while phylum Bacteroidetes in the colon cancer group. Bacterial genera Megamonas, Megasphaera, Mitsuokella, and Streptococcus were significantly abundant in the healthy group and Veillonella, Prevotella, and Eubacterium in the colon cancer group. Bacterial genus Bradyrhizobium was present in the healthy group and Alistipes, Coprococcus, Dorea, and Rhodococcus were present in the colon cancer group but absent in the healthy group.
CONCLUSION
There was a considerable difference in bacterial diversity in both the study groups indicating dysbiosis in the colon cancer group.
Topics: Colonic Neoplasms; Dysbiosis; Feces; Gastrointestinal Microbiome; Humans; Microbiota; RNA, Ribosomal, 16S
PubMed: 35381769
DOI: 10.4103/0973-1482.341139 -
Frontiers in Microbiology 2020The specific etiology and pathogenesis of oral lichen planus (OLP) remain elusive, and microbial dysbiosis may play an important role in OLP. We evaluated the saliva and...
The specific etiology and pathogenesis of oral lichen planus (OLP) remain elusive, and microbial dysbiosis may play an important role in OLP. We evaluated the saliva and tissue bacterial community of patients with OLP and identified the colonization of bacteria in OLP tissues. The saliva ( = 60) and tissue ( = 24) samples from OLP patients and the healthy controls were characterized by 16S rDNA gene sequencing and the bacterial signals in OLP tissues were detected by fluorescence hybridization (FISH) targeting the bacterial 16S rDNA gene. Results indicate that the OLP tissue microbiome was different from the microbiota of OLP saliva. Compared with the healthy controls, and were higher in OLP saliva, while - and were higher in OLP tissues, whereas seven taxa, including Carnobacteriaceae, Flavobacteriaceae, and , were enriched in both saliva and tissues of OLP patients. Furthermore, FISH found that the average optical density (AOD) of bacteria in the lamina propria of OLP tissues was higher than that of the healthy controls, and the AOD of bacteria in OLP epithelium and lamina propria was positively correlated. These data provide a different perspective for future investigation on the OLP microbiome.
PubMed: 32435231
DOI: 10.3389/fmicb.2020.00629 -
Frontiers in Microbiology 2022Acute radiation-induced esophagitis (ARIE) is one of the most debilitating complications in patients who receive thoracic radiotherapy, especially those with esophageal...
BACKGROUND
Acute radiation-induced esophagitis (ARIE) is one of the most debilitating complications in patients who receive thoracic radiotherapy, especially those with esophageal cancer (EC). There is little known about the impact of the characteristics of gut microbiota on the initiation and severity of ARIE.
MATERIALS AND METHODS
Gut microbiota samples of EC patients undergoing radiotherapy ( = 7) or concurrent chemoradiotherapy ( = 42) were collected at the start, middle, and end of the radiotherapy regimen. Assessment of patient-reported ARIE was also performed. Based on 16S rRNA gene sequencing, changes of the gut microbial community during the treatment regimen and correlations of the gut microbiota characteristics with the severity of ARIE were investigated.
RESULTS
There were significant associations of several properties of the gut microbiota with the severity of ARIE. The relative abundance of several genera in the phylum Proteobacteria increased significantly as mucositis severity increased. The predominant genera had characteristic changes during the treatment regimen, such as an increase of opportunistic pathogenic bacteria including . Patients with severe ARIE had significantly lower alpha diversity and a higher abundance of before radiotherapy, but patients with mild ARIE were enriched in , , , , , and . A model combining these genera had the best performance in prediction of severe ARIE (area under the curve: 0.907).
CONCLUSION
The characteristics of gut microbiota before radiotherapy were associated with subsequent ARIE severity. Microbiota-based strategies have potential use for the early prediction of subsequent ARIE and for the selection of interventions that may prevent severe ARIE.
PubMed: 35756007
DOI: 10.3389/fmicb.2022.883650 -
The Journal of Infectious Diseases Jun 2022A 25-mg dapivirine vaginal ring has been demonstrated to reduce risk of human immunodeficiency virus (HIV) acquisition in nonpregnant adult women. In this secondary...
BACKGROUND
A 25-mg dapivirine vaginal ring has been demonstrated to reduce risk of human immunodeficiency virus (HIV) acquisition in nonpregnant adult women. In this secondary analysis of studies conducted in US adolescent, lactating, and postmenopausal females, vaginal microbiota was assessed prior to and after ring use, and between dapivirine and placebo ring users.
METHODS
Vaginal fluid swabs were collected before and after product use for the evaluation of microbiota using Nugent criteria, quantitative culture, and quantitative polymerase chain reaction.
RESULTS
Vaginal ring use did not impact bacterial vaginosis prevalence among the 3 populations and was associated with minimal shifts in microbiota. Adolescents in both arms demonstrated an increased prevalence of Lactobacillus crispatus and a decrease in quantity of Megasphaera lornae. Postmenopausal active and placebo ring users demonstrated an increased prevalence of lactobacilli and non-albicans yeast, while dapivirine ring users demonstrated an increased prevalence of Candida albicans and increased quantity of group B Streptococcus and non-albicans yeasts. Prevotella species were increased in lactating women, whereas Prevotella timonensis increased in prevalence and concentration among adolescent and postmenopausal females and Prevotella bivia increased in prevalence among adolescent dapivirine ring users.
CONCLUSIONS
Dapivirine vaginal ring use was associated with minimal changes in the vaginal microbiota that are likely not clinically significant.
Topics: Adolescent; Adult; Contraceptive Devices, Female; Female; Humans; Lactation; Microbiota; Postmenopause; Pyrimidines; Vagina
PubMed: 34865071
DOI: 10.1093/infdis/jiab590 -
NPJ Biofilms and Microbiomes Sep 2022The cervicovaginal microbiome (CVM) correlates with women's cervical health, and variations in its composition are associated with high-risk human papillomavirus (hrHPV)...
The cervicovaginal microbiome (CVM) correlates with women's cervical health, and variations in its composition are associated with high-risk human papillomavirus (hrHPV) infection outcomes. Cervicovaginal microbes have been grouped into five community state types (CSTs) based on microbial community composition and abundance. However, studying the impact of CSTs in health and disease is challenging because the current sequencing technologies have limited confident discrimination between closely related and yet functionally different bacterial species. Circular probe-based RNA sequencing (ciRNAseq) achieves high-resolution microbiome profiling and therefore provides in-depth and unambiguous knowledge about the composition of the CVM. Based on ciRNAseq profiling of a large cohort of cervical smears (n = 541), we here define subgroups of CSTs I, III, and IV based on intra-CST differences with respect to abundances of Lactobacillus acidophilus (CSTs I-A vs. I-B and CSTs III-A vs. III-B), Lactobacillus iners (CSTs I-A vs. I-B and CSTs III-A vs. III-B), and Megasphaera genomosp type 1 (CSTs IV-A vs. IV-B). Our results further support the existence of subgroups of CST IV-C that are dominant for non-Lactobacillus species and have intermediate microbial diversity. We also show that CST V is associated with uninfected conditions, and CST IV-A associates with hrHPV-induced cervical disease. In conclusion, we characterized new subdivisions of cervicovaginal CSTs, which may further advance our understanding of women's cervical health and hrHPV-related progression to disease.
Topics: Female; Humans; Microbiota; RNA, Ribosomal, 16S; Sequence Analysis, RNA; Vagina
PubMed: 36171433
DOI: 10.1038/s41522-022-00336-6