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Frontiers in Microbiology 2021Current microbiome profiling of type 1 diabetes mellitus (T1D) patients is mostly limited to gut microbiome. We characterized the oral microbiome associated with T1D in...
Current microbiome profiling of type 1 diabetes mellitus (T1D) patients is mostly limited to gut microbiome. We characterized the oral microbiome associated with T1D in children after the onset of the disease and explored its relationship with oral physiological factors and dental status. This cohort study comprised 37 children aged 5-15 years with T1D and 29 healthy children matched in age and gender. Unstimulated whole saliva was collected from diabetic and non-diabetic children, in the morning after brushing their teeth and a fasting period of at least 1 h before sampling. 16S rRNA gene-based analysis was performed by Powersoil Pro kit by Qiagen and Phusion High-Fidelity PCR Master Mix. Oral physiological and dental parameters studied included decayed, missing, and filled teeth index, salivary flow rate, and salivary pH, glucose, calcium, phosphate, and urea levels. Of the identified 105 different genera and 211 different species, the most abundant genera were , , , , and . was more abundant in T1D children. The diabetes group had 22 taxa at the genus level and 33 taxa at the species level that were not present in the control group and the control group exhibited 6 taxa at the genus level and 9 taxa at the species level that did not exist in the diabetes group. In addition, , , and differed between healthy and T1D subjects. Eight species and eight subspecies were significantly more abundant among healthy children than in T1D children. and genera were significantly correlated with salivary parameters. We found similarities between taxa revealed in the present study and those found in gut microbiome in type 1 diabetes mellitus according to gutMDisorder database. Salivary microbiome analysis revealed unique microbial taxa that differed between T1D children and healthy subjects. Several genera found in the saliva of T1D children were associated with gut microbiome in T1D individuals.
PubMed: 34777313
DOI: 10.3389/fmicb.2021.756808 -
Microorganisms Sep 2021Periodontal and Endodontic diseases are biofilm-related diseases. The presence of microorganisms in root canals (RCs) and the complex microbiota of periodontal pockets...
Periodontal and Endodontic diseases are biofilm-related diseases. The presence of microorganisms in root canals (RCs) and the complex microbiota of periodontal pockets (PPs) contribute to the development of endodontic-periodontal diseases. This study performed a systemic analysis using state-of-the-art sequence data to assess the microbial composition of infected RCs and PPs to further assess the microbiota and verify the possibility of cross-infection between these sites. The microbiomes of these combined diseases were examined with a focus on the V3-V4 hypervariable region of the 16S rRNA gene. The number of species in PP was higher than in RC, and there was a predominance of obligate anaerobes and gram-negative bacteria. In the RCs, the genera , , predominated, in contrast, the PPs revealed a predominance of , , , and The RC and PP microbiome was not similar with regards to the sharing of OTUs for phyla and genera (8 and 67, respectively). The evaluation of molecular markers revealed a large number of markers for resistance to antibiotics of the carbapenem and beta-lactam type (broad spectrum). Another relevant finding of this study was the markers related to systemic diseases related to cardiac muscle and rheumatology, among others. In conclusion, the RC microbiota was less complex and diverse than PP. Interactions between microbial communities were present. The shared genus can signal communication between the endodontic and periodontal microbiomes.
PubMed: 34576820
DOI: 10.3390/microorganisms9091925 -
Frontiers in Microbiology 2021More and more studies have indicated that gut microbiota takes part in the biosynthesis and metabolism of sex hormones. Inversely, sex hormones influence the composition...
More and more studies have indicated that gut microbiota takes part in the biosynthesis and metabolism of sex hormones. Inversely, sex hormones influence the composition of gut microbiota. However, whether microbiota in the gut and vagina is associated with estrus return of weaning sows is largely unknown. Here, using 16S rRNA gene sequencing in 158 fecal and 50 vaginal samples, we reported the shifts in the gut and vaginal microbiota between normal return and non-return sows. In fecal samples, and S24-7 were enriched in normal return sows, while , Lachnospiraceae, , and had higher abundance in non-return sows. In vaginal swabs, the operational taxonomic units (OTUs) annotated to Clostridiales, Ruminoccaceae, and were enriched in normal return sows, while those OTUs annotated to , , , , and had higher abundances in non-return sows. Co-abundance group (CAG) analysis repeated the identification of the bacterial taxa associated with the estrus return of weaning sows. The predicted functional capacities in both gut and vaginal microbiome were changed between normal return and non-return sows. Serum metabolome profiles were determined by non-targeted metabolome analysis in seven normal return and six non-return sows. The metabolite features having higher abundance in normal return sows were enriched in the pathways Steroid hormone biosynthesis, Starch and sucrose metabolism, Galactose metabolism, and Vitamin B6 metabolism, while the metabolite features belonging to organic acids and derivatives, indoles and derivatives, sulfoxides, and lignans and neolignans had significantly higher abundance in non-return sows. Correlation analysis found that the changes in gut microbiota were associated with the shifts of serum metabolites and suggested that certain bacteria might affect estrus return of weaning sow through serum metabolites. These findings may provide new insights for understanding the role of the gut and vaginal microbiota in sow return to estrus after weaning.
PubMed: 34489885
DOI: 10.3389/fmicb.2021.690091 -
Journal of Dental Research Mar 2022An intuitive, clinically relevant index of microbial dysbiosis as a summary statistic of subgingival microbiome profiles is needed. Here, we describe a subgingival...
An intuitive, clinically relevant index of microbial dysbiosis as a summary statistic of subgingival microbiome profiles is needed. Here, we describe a subgingival microbial dysbiosis index (SMDI) based on machine learning analysis of published periodontitis/health 16S microbiome data. The raw sequencing data, split into training and test sets, were quality filtered, taxonomically assigned to the species level, and centered log-ratio transformed. The training data set was subject to random forest analysis to identify discriminating species (DS) between periodontitis and health. DS lists, compiled by various "Gini" importance score cutoffs, were used to compute the SMDI for samples in the training and test data sets as the mean centered log-ratio abundance of periodontitis-associated species subtracted by that of health-associated ones. Diagnostic accuracy was assessed with receiver operating characteristic analysis. An SMDI based on 49 DS provided the highest accuracy with areas under the curve of 0.96 and 0.92 in the training and test data sets, respectively, and ranged from -6 (most normobiotic) to 5 (most dysbiotic) with a value around zero discriminating most of the periodontitis and healthy samples. The top periodontitis-associated DS were spp., and , while and were the top health-associated DS. The index was highly reproducible by hypervariable region. Applying the index to additional test data sets in which nitrate had been used to modulate the microbiome demonstrated that nitrate has dysbiosis-lowering properties in vitro and in vivo. Finally, 3 genera (, and ) were identified that could be used for calculation of a simplified SMDI with comparable accuracy. In conclusion, we have developed a nonbiased, reproducible, and easy-to-interpret index that can be used to identify patients/sites at risk of periodontitis, to assess the microbial response to treatment, and, importantly, as a quantitative tool in microbiome modulation studies.
Topics: Dysbiosis; Humans; Microbiota; Periodontitis; RNA, Ribosomal, 16S; Treponema denticola
PubMed: 34428955
DOI: 10.1177/00220345211035775 -
Frontiers in Microbiology 2021Intestinal infections are a major cause of morbidity and mortality in humans and agricultural animals, especially newborns and weaned animals. Preventive treatments that...
Intestinal infections are a major cause of morbidity and mortality in humans and agricultural animals, especially newborns and weaned animals. Preventive treatments that help weaned animals maintain homeostasis and balance the hindgut microbial populations are desirable. The present study aimed to explore the impact of bacitracin methylene disalicylate (BMD) on the intestinal health by analyzing the intestinal environment, morphology, expression of peptidoglycan recognition proteins (PGRPs), and flora of weaned rabbits. A total of 300 New Zealand weaned rabbits were randomly divided into the following five treatment groups for a 35-day feed trial: control group (basal diet), bacitracin zinc (BZ) group (50 mg/kg BZ), BMDa group (100 mg/kg BMD), BMDb group (50 mg/kg BMD), and BMDc group (rabbits fed a basal diet supplemented with 25 mg/kg BMD). In each treatment group, 28 rabbits were slaughtered for experimental analysis. The results showed that the supplementation of BMD increased the environmental acidity of the cecum of the weaned rabbits and reduced the ammonia-nitrogen concentration, which was beneficial to the survival of useful bacteria in the intestine. The morphology analysis of the duodenum using hematoxylin and eosin staining revealed that the villus length, villus/crypt ratio, and intestinal wall thickness increased in the BMD group, thereby improving the structure of the duodenum and the absorption capacity of the small intestine. Moreover, real-time polymerase chain reaction test showed that PGRPs (especially PGLYRP-1 and PGLYRP-2) in the intestinal had an antagonistic effect with BMD in the process of inhibiting pathogenic bacteria, resulting in their decreased expression ( < 0.05). Furthermore, through 16S rRNA sequencing in the cecal content, the abundance of the predominant phyla in the BMDa and BZ groups was found to be the closest. The abundance of the genera , ), (), , (), , , and increased in the BMDa and BZ groups ( < 0.05). The relative abundance of , , and significantly increased only in the BMDa group ( < 0.05). Conclusively, BMD, as well as microbes, improved the intestinal environment and structure to maintain the intestinal health of weaned rabbits.
PubMed: 34248860
DOI: 10.3389/fmicb.2021.579006 -
Animal : An International Journal of... Mar 2021The caecum is the primary site where microbial fermentation and acidosis occurred. The supplementation of starter feed and alfalfa hay has the potential to influence...
The caecum is the primary site where microbial fermentation and acidosis occurred. The supplementation of starter feed and alfalfa hay has the potential to influence caecal microbiota and then affect caecal fermentation. This study aims to investigate the effect of starter feed and alfalfa hay supplementation on caecal microbiota, immune homeostasis, and growth of preweaning yaks. Twenty 30-day-old male yak calves were randomly assigned to four groups, which separately fed with milk replacer (CON group), milk replacer with alfalfa hay (A group), milk replacer with starter feed (S group), and milk replacer with starter feed plus alfalfa hay (SA group) throughout the trial. Growth performance and plasma physiological and biochemical indicators were measured every 30 days. Calves were sacrificed at 120 days of age. The caecal contents were collected for measuring pH and contents of volatile fatty acids (VFAs) and lipopolysaccharide (LPS) and for characterizing caecal microbiota. The results indicated that individual or simultaneous supplementation with alfalfa hay and starter feed all significantly increased the BW, body height, body length, and chest girth of yak calves. However, supplementation with starter feed significantly increased plasma cortisol, nitric oxide, tumor necrosis factor-α, and interferon-γ concentrations and the ratio of aspartate aminotransferase to alanine aminotransferase of yak calves when compared with the control and alfalfa hay feeding groups, while the co-supplementation of starter feed and alfalfa hay could significantly decrease these inflammation-related indices when compared with the starter feeding group. Sequencing of the 16S rRNA gene showed that starter feed and alfalfa hay separately stimulated the proliferation of starch-decomposing and cellulose- or hemicellulose-decomposing bacteria. This also significantly increased the levels of acetate, propionate, butyrate, valerate, isobutyrate, and isovalerate in the caecal contents. Furthermore, compared with the S and CON groups, the significantly increased genera of Desulfobulbus, Olsenella, Pseudoflavonifractor, and Stomatobaculum in the SA and A groups were beneficial to the immune homeostasis, and the significantly decreased Blautia, Clostridium IV, Bacteroides, Eubacterium, Clostridium XVIII, and Mogibacterium in the SA and A groups were related to the reduced caecal lactate and LPS contents, the decreased inflammatory reaction, and the improved healthy hepatic condition of yak calves. In conclusion, milk replacer supplemented with alfalfa hay and starter feed is recommended during preweaning to improve yak calf health and growth because this regimen promotes the growth and maintains the immune homeostasis of yak calves.
Topics: Animal Feed; Animals; Body Weight; Cattle; Cecum; Diet; Dietary Supplements; Fermentation; Male; Medicago sativa; Microbiota; RNA, Ribosomal, 16S; Rumen; Weaning
PubMed: 33610512
DOI: 10.1016/j.animal.2020.100019 -
Journal of Oral Microbiology Nov 2020: Refractory infection is an important factor affecting the progression of medication-related osteonecrosis of the jaw (MRONJ) from clinical stage I to stage II/III. The...
: Refractory infection is an important factor affecting the progression of medication-related osteonecrosis of the jaw (MRONJ) from clinical stage I to stage II/III. The aim of this study was to explore the distribution of bacteria and their association with the inflammatory pathway of stage II/III MRONJ. : Nine specimens of fresh inflammation tissue, located next to the necrotic bone or sequestrum, were collected from MRONJ patients. Nine specimens from normal oral mucosa were collected from healthy patients. The 16S rRNA gene sequencing method was used to determine the distribution characteristics of the bacterial colony. The protein microarray analysis was used to detect the expression of inflammatory cytokines. : The average relative abundance of , and was higher, while and were lower in the MRONJ group. Most pro-inflammatory cytokines were up-regulated in the MRONJ group; yet, only IFNγ, TNFα, and IL8 showed statistical differences ( < 0.05). and were positively correlated with IL8, and was positively correlated with IFNγ and TNFα. : IL8/IFNγ/TNFα pro-inflammatory effect caused by , and may be the leading cause of advancing MRONJ and thus may be used as a new target for infection control.
PubMed: 33391627
DOI: 10.1080/20002297.2020.1851112 -
Cancer Prevention Research... Mar 2021Given the increasing evidence that the oral microbiome is involved in obesity, diabetes, and cancer risk, we investigated baseline oral microbiota profiles in relation...
Given the increasing evidence that the oral microbiome is involved in obesity, diabetes, and cancer risk, we investigated baseline oral microbiota profiles in relation to all-cancer incidence among nonsmoking women enrolled in a Texas cohort of first- and second-generation immigrants of Mexican origin. We characterized the 16Sv4 rDNA microbiome in oral mouthwash samples collected at baseline from a representative subset of 305 nonsmoking women, ages 20-75 years. We evaluated within- (alpha) and between-sample (beta) diversity by incident cancer status and applied linear discriminant analysis (LDA) effect size analysis to assess differentially abundant taxa. Diversity and candidate taxa in relation to all-cancer incidence were evaluated in multivariable-adjusted Cox regression models. Over 8.8 median years of follow-up, 31 incident cancer cases were identified and verified. Advanced age, greater acculturation, and cardiometabolic risk factors were associated with all-cancer incidence. Higher alpha diversity (age-adjusted < 0.01) and distinct biological communities ( = 0.002) were observed by incident cancer status. Each unit increase in the Shannon diversity index yielded >8-fold increase in all-cancer and obesity-related cancer risk [multivariable-adjusted HR (95% confidence interval), 8.11 (3.14-20.94) and 10.72 (3.30-34.84), respectively] with similar findings for the inverse Simpson index. was enriched among women who did not develop cancer, while , and were higher among women who developed cancer (LDA score ≥ 3; q-value < 0.01). This initial study of oral microbiota and overall cancer risk in nonsmoking Mexican American women suggests the readily accessible oral microbiota as a promising biomarker. PREVENTION RELEVANCE: Mexican American women suffer a disproportionate burden of chronic health conditions that increase cancer risk. Few investigations of the microbiome, a key determinant of host health, have been conducted among this group. Oral microbiota profiles may provide early and accessible cancer biomarker data on invasive bacteria or community disruptions.
Topics: Adult; Aged; Bacteria; Dysbiosis; Female; Follow-Up Studies; Humans; Incidence; Mexican Americans; Microbiota; Middle Aged; Mouth; Neoplasms; Prognosis; Prospective Studies; Texas; Young Adult
PubMed: 33277317
DOI: 10.1158/1940-6207.CAPR-20-0405 -
Frontiers in Cellular and Infection... 2020The oral microbiota has been connected to the pathogenesis of rheumatoid arthritis through activation of mucosal immunity. The objective of this study was to...
BACKGROUND
The oral microbiota has been connected to the pathogenesis of rheumatoid arthritis through activation of mucosal immunity. The objective of this study was to characterize the salivary oral microbiome associated with juvenile idiopathic arthritis (JIA), and correlate it with the disease activity including gingival inflammation.
METHODS
Fifty-nine patients with JIA (mean age, 12.6 ± 2.7 years) and 34 healthy controls (HC; mean age 12.3 ± 3.0 years) were consecutively recruited in this Norwegian cross-sectional study. Information about demographics, disease activity, medication history, frequency of tooth brushing and a modified version of the gingival bleeding index (GBI) and the simplified oral hygiene index (OHI-S) was obtained. Microbiome profiling of saliva samples was performed by sequencing of the V1-V3 region of the 16S rRNA gene, coupled with a species-level taxonomy assignment algorithm; QIIME, LEfSe and R-package for Spearman correlation matrix were used for downstream analysis.
RESULTS
There were no significant differences between JIA and HC in alpha- and beta-diversity. However, differential abundance analysis revealed several taxa to be associated with JIA: , and at the genus level; and oral taxon 417, oral taxon 352 and oral taxon 864 among others, at the species level. species, oral taxon 223, and , were associated with healthy controls. , sp. oral taxon 498 and oral taxon 914 correlated positively with the composite juvenile arthritis 10-joint disease activity score (JADAS10), while oral taxon 44 among others, correlated with the number of active joints. Of all microbial markers identified, only and oral taxon 44 maintained false discovery rate (FDR) < 0.1.
CONCLUSIONS
In this exploratory study of salivary oral microbiome we found similar alpha- and beta-diversity among children with JIA and healthy. Several taxa associated with chronic inflammation were found to be associated with JIA and disease activity, which warrants further investigation.
Topics: Adolescent; Arthritis, Juvenile; Case-Control Studies; Child; Cross-Sectional Studies; Gemella; Humans; Microbiota; RNA, Ribosomal, 16S
PubMed: 33251163
DOI: 10.3389/fcimb.2020.602239 -
Animals : An Open Access Journal From... Nov 2020Roughage particle size can influence rumen development, which is also determined by rumen microorganisms and their metabolic end-products. Therefore, the aim of this...
Roughage particle size can influence rumen development, which is also determined by rumen microorganisms and their metabolic end-products. Therefore, the aim of this study was to evaluate the comprehensive effects of roughage length and rumen bacterial community on the rumen development of weaned calves. A total of thirty-six weaned Angus female calves (125 ± 3 d; 161.2 ± 13.0 kg) were randomly assigned to three diets differing in roughage particle size: 4 cm (short length); 24 cm (medium length); and 44 cm (long length). Results showed that chopping roughage increased dry matter intake and organic matter apparent digestibility; altered rumen fermentation indicated by the increased rumen butyrate and valerate concentrations; and increased plasma glucose, cholesterol, and total protein. Chopping roughage affected rumen bacterial community, as indicated by altering the diversity indices; by increasing ruminal bacteria and , which are involved in butyrate production; and by increasing and , which are involved in bacterial colonization. In conclusion, chopping roughage at 4 cm was shown to improve the rumen bacterial community, alter rumen fermentation, eventually promote the development of rumen.
PubMed: 33227931
DOI: 10.3390/ani10112149