-
Microbiome Oct 2020Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal...
BACKGROUND
Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal models. In addition, the shared and distinct microbiome features among complex human diseases remain largely unclear.
RESULTS
This analysis was based on a Chinese population with 1475 participants. We estimated the SNP-based heritability, which suggested that Desulfovibrionaceae and Odoribacter had significant heritability estimates (0.456 and 0.476, respectively). We performed a microbiome genome-wide association study to identify host genetic variants associated with the gut microbiome. We then conducted bidirectional Mendelian randomization analyses to examine the potential causal associations between the gut microbiome and complex human diseases. We found that Saccharibacteria could potentially decrease the concentration of serum creatinine and increase the estimated glomerular filtration rate. On the other hand, atrial fibrillation, chronic kidney disease and prostate cancer, as predicted by host genetics, had potential causal effects on the abundance of some specific gut microbiota. For example, atrial fibrillation increased the abundance of Burkholderiales and Alcaligenaceae and decreased the abundance of Lachnobacterium, Bacteroides coprophilus, Barnesiellaceae, an undefined genus in the family Veillonellaceae and Mitsuokella. Further disease-microbiome feature analysis suggested that systemic lupus erythematosus and chronic myeloid leukaemia shared common gut microbiome features.
CONCLUSIONS
These results suggest that different complex human diseases share common and distinct gut microbiome features, which may help reshape our understanding of disease aetiology in humans. Video Abstract.
Topics: Adult; Aged; Animals; Case-Control Studies; Disease; Female; Gastrointestinal Microbiome; Genome-Wide Association Study; Humans; Leukemia, Myelogenous, Chronic, BCR-ABL Positive; Lupus Erythematosus, Systemic; Male; Middle Aged
PubMed: 33032658
DOI: 10.1186/s40168-020-00923-9 -
Neuropsychiatric Disease and Treatment 2022By exploring the gut-related microbiota differences of adolescents with non-suicidal self-injury (NSSI) and depression (without NSSI) and healthy volunteers, we provide...
PURPOSE
By exploring the gut-related microbiota differences of adolescents with non-suicidal self-injury (NSSI) and depression (without NSSI) and healthy volunteers, we provide a theoretical basis for the prevention and control of NSSI in adolescents through intestinal microecological regulation.
PATIENTS AND METHODS
A total of 99 subjects were recruited in Guangdong Province, China, including 51 adolescents with NSSI (KD), 24 healthy adolescents (NOR1), and 24 depression adolescents without NSSI (NOR2). General clinical data and fecal samples were collected from all subjects, who were assessed using the NSSI Behavioral Questionnaire and the 24-item Hamilton Depression Scale. The taxonomic composition of the gut microbiota was determined using the 16S rDNA gene sequencing method.
RESULTS
There were significant differences in diversity between the KD and NOR1, and the species uniformity index of the KD according to the Shannon and Simpson indices was significantly reduced compared with that of the NOR1 (4.81 vs 5.21, p<0.01; 0.02 vs 0.01, p<0.05). The relative abundances were different among the KD, NOR1 and NOR2, as reflected at the taxonomic levels of class, order, family, genus, and species. Bacteroides were the dominant flora of the KD and NOR2, while Mitsuokella was the dominant flora that distinguished the KD from the NOR2.
CONCLUSION
We found that gut microbiota diversity was decreased in adolescents with NSSI, and the relative abundance was altered at different taxonomic levels. These results enrich the understanding of the relationship between NSSI and depression and the gut microbiota, Supporting that NSSI and depression are not homologous disorders. What is more, it establishes the basis for exploring the mechanisms of flora action in NSSI, providing a possible direction for NSSI to achieve a better prognosis and prevent relapse.
PubMed: 35799798
DOI: 10.2147/NDT.S360588 -
Journal of Pharmacy & Bioallied Sciences 2017Periodontitis is a polymicrobial disease caused by complex interactions between distinct pathogens in a biofilm resulting in the destruction of periodontal tissues. It... (Review)
Review
Periodontitis is a polymicrobial disease caused by complex interactions between distinct pathogens in a biofilm resulting in the destruction of periodontal tissues. It seems evident that unknown microorganisms might be involved in onset or progression of periodontitis. For many decades, research in the field of oral microbiology failed to identify certain subgingival microbiota due to technical limitations but, over a period of 12 years using molecular approaches and sequencing techniques, it became feasible to reveal the existence of new periodontal pathogens. Therefore, it is evident that in addition to conventional periodontal pathogens, other microbes might be involved in onset and progression of periodontitis. The novel pathogens enlisted under periodontal phylogeny include , , , , , , , , and . The polymicrobial etiology of periodontitis has been elucidated by comprehensive techniques, and studies throwing light on the possible virulence mechanisms possessed by these novel periodontal pathogens are enlisted.
PubMed: 28979069
DOI: 10.4103/jpbs.JPBS_288_16 -
Journal of Dairy Science Oct 2021In our previous studies, we revealed the effect of lactose inclusion in calf starters on the growth performance and gut development of calves. We conducted the present...
In our previous studies, we revealed the effect of lactose inclusion in calf starters on the growth performance and gut development of calves. We conducted the present study as a follow-up study to identify the shift in rumen microbiota and its relation to rumen fermentation when calves are fed a lactose-containing starter. Thirty Holstein bull calves were divided into 2 calf starter treatment groups: texturized calf starter (i.e., control; n = 15) or calf starter in which starch was replaced with lactose at 10% (i.e., LAC10; n = 15) on a dry matter basis. All calves were fed their respective treatment calf starter ad libitum from d 7, and kleingrass hay from d 35. Rumen digesta were collected on d 80 (i.e., 3 wk after weaning) and used to analyze rumen microbiota and fermentation products. There was no apparent effect of lactose feeding on the α-diversity and overall composition of rumen microbiota. Amplicon sequencing and real-time PCR quantification of the 16S rRNA gene confirmed that the abundance of butyrate-producing bacteria (i.e., Butyrivibrio group and Megasphaera elsdenii) did not differ between the control and LAC10 groups. Conversely, the relative abundance of Mitsuokella spp., which produce lactate, succinate, and acetate, was significantly higher in the rumen of calves that were fed lactose, whereas the lactate concentration did not differ between the control and LAC10 groups. These findings suggest that the lactate production can be elevated by an increase of Mitsuokella spp. and then converted into butyrate, not propionate, since the proportion of propionate was lower in lactose-fed calves. In addition, we observed a higher abundance of Coriobacteriaceae and Pseudoramibacter-Eubacterium in the LAC10 group. Both these bacterial taxa include acetate-producing bacteria, and a positive correlation between the acetate-to-propionate ratio and the abundance of Pseudoramibacter-Eubacterium was observed. Therefore, the higher abundance of Coriobacteriaceae, Mitsuokella spp., and Pseudoramibacter-Eubacterium in the rumen of lactose-fed calves partially explains the increase in the proportion of rumen acetate that was observed in our previous study.
Topics: Animal Feed; Animals; Body Weight; Cattle; Diet; Fermentation; Follow-Up Studies; Lactose; Male; Microbiota; RNA, Ribosomal, 16S; Rumen; Weaning
PubMed: 34218911
DOI: 10.3168/jds.2021-20225 -
PloS One 2022Fermentation of pasture grasses and grains in the rumen of dairy cows and other ruminants produces methane as a by-product, wasting energy and contributing to the...
Fermentation of pasture grasses and grains in the rumen of dairy cows and other ruminants produces methane as a by-product, wasting energy and contributing to the atmospheric load of greenhouse gasses. Many feeding trials in farmed ruminants have tested the impact of dietary components on feed efficiency, productivity and methane yield (MeY). Such diets remodel the rumen microbiome, altering bacterial, archaeal, fungal and protozoan populations, with an altered fermentation outcome. In dairy cows, some dietary grains can reduce enteric methane production. This is especially true of wheat, in comparison to corn or barley. Using a feeding trial of cows fed rolled wheat, corn or barley grain, in combination with hay and canola, we identified wheat-associated changes in the ruminal microbiome. Ruminal methane production, pH and VFA concentration data together with 16S rRNA gene amplicon sequences were used to compare ruminal bacterial and archaeal populations across diets. Differential abundance analysis of clustered sequences (OTU) identified members of the bacterial families Lachnospiraceae, Acidaminococcaceae, Eubacteriaceae, Prevotellaceae, Selenomonadaceae, Anaerovoracaceae and Fibrobacteraceae having a strong preference for growth in wheat-fed cows. Within the methanogenic archaea, (at >99% 16S rRNA sequence identity) the growth of Methanobrevibacter millerae was favoured by the non-wheat diets, while Methanobrevibacter olleyae was unaffected. From the wheat-preferring bacteria, correlation analysis found OTU strongly linked to reduced MeY, reduced pH and raised propionic acid levels. OTU from the genera Shuttleworthia and Prevotella_7 and especially Selenomonadaceae had high anti-methane correlations. An OTU likely representing (100% sequence identity) the fumarate-reducing, hydrogen-utilising, rumen bacterium Mitsuokella jalaludinii, had an especially high negative correlation coefficient (-0.83) versus MeY and moderate correlation (-0.6) with rumen pH, strongly suggesting much of the MeY suppression is due to reduced hydrogen availablity. Other OTU, representing as yet unknown species from the Selenomonadaceae family and the genera Prevotella_7, Fibrobacter and Syntrophococcus also had high to moderate negative MeY correlations, but low correlation with pH. These latter likely represent bacterial species able to reduce MeY without causing greater ruminal acidity, making them excellent candidates, provided they can be isolated, for development as anti-methane probiotics.
Topics: Animal Feed; Animals; Cattle; Diet; Female; Fermentation; Humans; Hydrogen; Lactation; Methane; Microbiota; Milk; Prevotella; RNA, Ribosomal, 16S; Rumen; Triticum; Zea mays
PubMed: 35587477
DOI: 10.1371/journal.pone.0268157 -
Frontiers in Microbiology 2022Antimicrobial chemicals are used as preservatives in cosmetics, pharmaceuticals, and food to prevent the growth of bacteria and fungi in the products. Unintentional...
Antimicrobial chemicals are used as preservatives in cosmetics, pharmaceuticals, and food to prevent the growth of bacteria and fungi in the products. Unintentional exposure in humans to such chemicals is well documented, but whether they also interfere with human oral microbiome composition is largely unexplored. In this study, we explored whether the oral bacterial composition is affected by exposure to antibacterial and environmental chemicals. Gingival fluid, urine, and interview data were collected from 477 adults (18-47 years) from the RHINESSA study in Bergen, Norway. Urine biomarkers of triclosan, triclocarban, parabens, benzophenone-3, bisphenols, and 2,4- and 2,5-dichlorophenols (DCPs) were quantified (by mass spectrometry). Microbiome analysis was based on 16S amplicon sequencing. Diversity and differential abundance analyses were performed to identify how microbial communities may change when comparing groups of different chemical exposure. We identified that high urine levels (>75th percentile) of propyl parabens were associated with a lower abundance of bacteria genera , and , as compared with low propylparaben levels (<25 percentile). High exposure to ethylparaben was associated with a higher abundance of . High urine levels of bisphenol A were associated with a lower abundance of and exposure to another environmental chemical, 2,4-DCP, was associated with a lower abundance of , and . High exposure to antibacterial and environmental chemicals was associated with an altered composition of gingiva bacteria; mostly commensal bacteria in the oral cavity. Our results highlight a need for a better understanding of how antimicrobial chemical exposure influences the human microbiome.
PubMed: 35572708
DOI: 10.3389/fmicb.2022.790496 -
Frontiers in Microbiology 2019has a positive effect on the host intestinal microbiota. In piglets, dietary supplementation with affects general health and plays an important role in nutrient...
has a positive effect on the host intestinal microbiota. In piglets, dietary supplementation with affects general health and plays an important role in nutrient digestion and fermentation. However, this association requires further investigation. Here, we studied newborn piglets from 12 litters. The nursed piglets were given a creep feed beginning on day 10 and weaned at day 30. Piglets were fed either a control basic diet or a diet including supplementation with ZLR003 at 6.0 × 10 CFU/g feed. At day 30 and 60, feces samples were taken and used for sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. At day 60, feces samples and serum samples were also taken and used to measure the short chain fatty acids (SCFAs) and to detect long chain fatty acids (LCFAs) and free amino acids (FAAs), respectively. The results revealed that ZLR003 could improve piglet fecal microbiota composition, especially at the end of weaned period. The concentrations of lactic acid and butyric acid in feces were higher, and acetic acid concentration was lower in the ZLR003 group compared with the control group ( < 0.05). The serum polyunsaturated fatty acids C18:2n6c, C18:3n3, C20:4n6, and C22:6n3 were significantly higher ( < 0.05), as were the serum FAAs Gly, Ala, Val, Iso, Asn, Asp, Glu, Met, Phe, and Leu ( < 0.05), in the group compared with the control group. A correlation analysis revealed that the genera _UCG-010 and _UCG-014 had a negative correlation with the SCFAs content in feces, the genus _9 had a higher positive correlation with C18:2n6c, and the genera and had a more positive significant effect on the serum FAAs content in weaned piglets in the ZLR003 group compared with the control group. In conclusion, ZLR003 influenced the fecal microbiota composition of piglets, and its effects were related to the metabolism of SCFAs, LCFAs, and FAAs. Our findings will help facilitate the application of strains in pig production.
PubMed: 31040835
DOI: 10.3389/fmicb.2019.00785 -
Clinical and Experimental Dental... Feb 2022It has been suggested that smoking affects the oral microbiome, but its effects on sites other than the subgingival microbiome remain unclear. This study investigated...
OBJECTIVES
It has been suggested that smoking affects the oral microbiome, but its effects on sites other than the subgingival microbiome remain unclear. This study investigated the composition of the salivary and tongue bacterial communities of smokers and nonsmokers in periodontally healthy adults.
METHODS
The study population included 50 healthy adults. The bacterial composition of resting saliva and the tongue coating was identified through barcoded pyrosequencing analysis of the 16S rRNA gene. The Brinkman index (BI) was used to calculate lifetime exposure to smoking. The richness and diversity of the microbiome were evaluated using the t-test. Differences in the proportions of bacterial genera between smokers and nonsmokers were evaluated using the Mann-Whitney U test. The quantitative relationship between the proportions of genera and the BI was evaluated using Pearson's correlation analysis.
RESULTS
The richness and diversity of the oral microbiome differed significantly between saliva and the tongue but not between smokers and nonsmokers. The saliva samples from smokers were enriched with the genera Treponema and Selenomonas. The tongue samples from smokers were enriched with the genera Dialister and Atopobium. The genus Cardiobacterium in saliva, and the genus Granulicatella on the tongue, were negatively correlated with BI values. On the other hand, the genera Treponema, Oribacterium, Dialister, Filifactor, Veillonella, and Selenomonas in saliva and Dialister, Bifidobacterium, Megasphaera, Mitsuokella, and Cryptobacterium on the tongue were positively correlated with BI values.
CONCLUSIONS
The saliva and tongue microbial profiles of smokers and nonsmokers differed in periodontally healthy adults. The genera associated with periodontitis and oral malodor accounted for high proportions in saliva and on the tongue of smokers without periodontitis and were positively correlated with lifetime exposure to smoking. The tongue might be a reservoir of pathogens associated with oral disease in smokers.
Topics: Adult; Bacteria; Cigarette Smoking; Humans; Microbiota; Periodontitis; RNA, Ribosomal, 16S; Tongue
PubMed: 34505401
DOI: 10.1002/cre2.489 -
Scientific Reports Jun 2022Bacterial colonization in the rumen of pre-weaned ruminants is important for their growth and post-weaning productivity. This study evaluated the effects of oral fiber...
Bacterial colonization in the rumen of pre-weaned ruminants is important for their growth and post-weaning productivity. This study evaluated the effects of oral fiber administration during the pre-weaning period on the development of rumen microbiota from pre-weaning to the first lactation period. Twenty female calves were assigned to control and treatment groups (n = 10 each). Animals in both groups were reared using a standard feeding program throughout the experiment, except for oral fiber administration (50-100 g/day/animal) from 3 days of age until weaning for the treatment group. Rumen content was collected during the pre-weaning period, growing period, and after parturition. Amplicon sequencing of the 16S rRNA gene revealed that oral fiber administration facilitated the early establishment of mature rumen microbiota, including a relatively higher abundance of Prevotella, Shuttleworthia, Mitsuokella, and Selenomonas. The difference in the rumen microbial composition between the dietary groups was observed even 21 days after parturition, with a significantly higher average milk yield in the first 30 days of lactation. Therefore, oral fiber administration to calves during the pre-weaning period altered rumen microbiota, and its effect might be long-lasting until the first parturition.
Topics: Animal Feed; Animals; Cattle; Diet; Dietary Fiber; Female; Lactation; Microbiota; Milk; RNA, Ribosomal, 16S; Rumen; Weaning
PubMed: 35750897
DOI: 10.1038/s41598-022-15155-0 -
PloS One 2022Although some human studies have reported gut microbiome changes in individuals with Alzheimer's disease (AD) dementia or mild cognitive impairment (MCI), gut microbiome...
BACKGROUND
Although some human studies have reported gut microbiome changes in individuals with Alzheimer's disease (AD) dementia or mild cognitive impairment (MCI), gut microbiome alterations in preclinical AD, i.e., cerebral amyloidosis without cognitive impairment, is largely unknown.
OBJECTIVE
We aimed to identify gut microbial alterations associated with preclinical AD by comparing cognitively normal (CN) older adults with cerebral Aβ deposition (Aβ+ CN) and those without cerebral Aβ deposition (Aβ- CN).
METHODS
Seventy-eight CN older participants (18 Aβ+ CN and 60 Aβ- CN) were included, and all participants underwent clinical assessment and Pittsburg compound B-positron emission tomography. The V3-V4 region of the 16S rRNA gene of genomic DNA extracted from feces was amplified and sequenced to establish the microbial community.
RESULTS
Generalized linear model analysis revealed that the genera Megamonas (B = 3.399, q<0.001), Serratia (B = 3.044, q = 0.005), Leptotrichia (B = 5.862, q = 0.024) and Clostridium (family Clostridiaceae) (B = 0.788, q = 0.034) were more abundant in the Aβ+ CN group than the Aβ- CN group. In contrast, genera CF231 (B = -3.237, q< 0.001), Victivallis (B = -3.447, q = 0.004) Enterococcus (B = -2.044, q = 0.042), Mitsuokella (B = -2.119, q = 0.042) and Clostridium (family Erysipelotrichaceae) (B = -2.222, q = 0.043) were decreased in Aβ+ CN compared to Aβ- CN. Notably, the classification model including the differently abundant genera could effectively distinguish Aβ+ CN from Aβ- CN (AUC = 0.823).
CONCLUSION
Our findings suggest that specific alterations of gut bacterial taxa are related to preclinical AD, which means these changes may precede cognitive decline. Therefore, examining changes in the microbiome may be helpful in preclinical AD screening.
Topics: Humans; Animals; Aged; Gastrointestinal Microbiome; Alzheimer Disease; RNA, Ribosomal, 16S; Tomography, X-Ray Computed; Cognitive Dysfunction
PubMed: 36445883
DOI: 10.1371/journal.pone.0278276