Journal articles: 'Microbial association'

1

Lo, Chieh, and Radu Marculescu. "MPLasso: Inferring microbial association networks using prior microbial knowledge." PLOS Computational Biology 13, no. 12 (December 27, 2017): e1005915. http://dx.doi.org/10.1371/journal.pcbi.1005915.

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Soja, Constance M., and Robert Riding. "Silurian microbial associations from the Alexander terrane, Alaska." Journal of Paleontology 67, no. 5 (September 1993): 728–38. http://dx.doi.org/10.1017/s0022336000037021.

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Silurian calcareous algae, cyanobacteria, and microproblematica are abundantly preserved in the Alexander terrane of southeastern Alaska. They represent a diverse population of calcified microbes that contributed to the formation of a variety of shallow- and deep-water carbonate deposits. Five associations are recognized on the basis of recurring groups of microbial taxa. These include a Girvanella-Tuxekanella association that formed oncoids and thick encrustations on skeletal grains in shelf environments. A Renalcis association predominated in a stromatoporoid-coral reef that developed at the incipient shelf margin on a crinoid-solenoporid shoal (“Solenopora” association). Other organic buildups are characterized by a Ludlovia association, which constructed skeletal stromatolite reefs, and by an Epiphyton-Sphaerina association that contributed to the formation of a stromatolitic mud mound. A mixed microbial assemblage reflects transport and mixing of shallow-water microbial biotas that were deposited by turbidity currents, debris flows, and slumps in a slope environment.

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Wang, Yiqing, Huijun Wang, Annie Green Howard, Katie A. Meyer, Matthew C. B. Tsilimigras, Christy L. Avery, Wei Sha, et al. "Circulating Short-Chain Fatty Acids Are Positively Associated with Adiposity Measures in Chinese Adults." Nutrients 12, no. 7 (July 17, 2020): 2127. http://dx.doi.org/10.3390/nu12072127.

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Epidemiological studies suggest a positive association between obesity and fecal short-chain fatty acids (SCFAs) produced by microbial fermentation of dietary carbohydrates, while animal models suggest increased energy harvest through colonic SCFA production in obesity. However, there is a lack of human population-based studies with dietary intake data, plasma SCFAs, gut microbial, and anthropometric data. In 490 Chinese adults aged 30–68 years, we examined the associations between key plasma SCFAs (butyrate/isobutyrate, isovalerate, and valerate measured by non-targeted plasma metabolomics) with body mass index (BMI) using multivariable-adjusted linear regression. We then assessed whether overweight (BMI ≥ 24 kg/m2) modified the association between dietary-precursors of SCFAs (insoluble fiber, total carbohydrates, and high-fiber foods) with plasma SCFAs. In a sub-sample (n = 209) with gut metagenome data, we examined the association between gut microbial SCFA-producers with BMI. We found positive associations between butyrate/isobutyrate and BMI (p-value < 0.05). The associations between insoluble fiber and butyrate/isobutyrate differed by overweight (p-value < 0.10). There was no statistical evidence for an association between microbial SCFA-producers and BMI. In sum, plasma SCFAs were positively associated with BMI and that the colonic fermentation of fiber may differ for adults with versus without overweight.

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Ai, Dongmei, Xiaoxin Li, Gang Liu, Xiaoyi Liang, and Li Xia. "Constructing the Microbial Association Network from Large-Scale Time Series Data Using Granger Causality." Genes 10, no. 3 (March 14, 2019): 216. http://dx.doi.org/10.3390/genes10030216.

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The increasing availability of large-scale time series data allows the inference of microbial community dynamics by association network analysis. However, correlation-based association network analyses are noninformative of causal, mediating and time-dependent relationships between microbial community functional factors. To address this insufficiency, we introduced the Granger causality model to the analysis of a recent marine microbial time series dataset. We systematically constructed a directed acyclic network, representing both internal and external causal relationships among the microbial and environmental factors. We further optimized the network by removing false causal associations using the conditional Granger causality. The final network was visualized as a Granger graph, which was analyzed to identify causal relationships driven by key functional operators in the environment, such as Gammaproteobacteria, which was Granger caused by total organic nitrogen and primary production (p < 0.05 and Q < 0.05).

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Hernández, M. A. González, E. E. Canfora, and E. E. Blaak. "Faecal microbial metabolites of proteolytic and saccharolytic fermentation in relation to degree of insulin resistance in adult individuals." Beneficial Microbes 12, no. 3 (June 15, 2021): 259–66. http://dx.doi.org/10.3920/bm2020.0179.

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The gut microbiota may affect host metabolic health through microbial metabolites. The balance between the production of microbial metabolites by saccharolytic and proteolytic fermentation may be an important determinant of metabolic health. Amongst the best-studied saccharolytic microbial metabolites are the short-chain fatty acids acetate, propionate and butyrate. However, human data on the role of other microbial fermentation by-products in metabolic health are greatly lacking. Therefore, we compared in a cross-sectional study the faecal microbial metabolites (caproate, lactate, valerate, succinate, and the branched-chain fatty acids (BCFA) (isobutyrate, isovalerate)) between insulin sensitive (homeostatic model assessment of insulin resistance (HOMA-IR), HOMA-IR<1.85, IS) and insulin resistant (HOMA-IR>1.85, IR) individuals. Additionally, we assessed the relationships between faecal metabolites and markers of metabolic health including fasting glucose, insulin, free fatty acids, insulin resistance (HOMA-IR) and fasting substrate oxidation in 86 individuals with a wide range of body mass index. Faecal metabolite concentrations did not significantly differ between IS and IR. Furthermore, there were no associations between microbial metabolites and metabolic health markers, except for a slight positive association of isovalerate with carbohydrate oxidation (E%, std β 0.194, P=0.011) and fat oxidation (E%, std β -0.075, P=0.047), also after adjustment for age, sex and BMI. In summary, faecal caproate, lactate, valerate, succinate, and BCFA (isobutyrate, isovalerate) were not different between IR and IS individuals, nor was there any association between these faecal metabolites and parameters of metabolic health. Further human intervention studies are warranted to investigate the role of these microbially-derived fermentation products and their kinetics in metabolic health and insulin sensitivity.

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Lee, Victoria. "Microbial Transformations." Historical Studies in the Natural Sciences 48, no. 4 (September 1, 2018): 441–74. http://dx.doi.org/10.1525/hsns.2018.48.4.441.

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The domestication of penicillin production in Japan was a priority for the Allied occupation government (1945–1952) immediately after World War II, since manufacturing the drug using raw materials available locally would lower the cost of the occupation. In place of employing the analytical concept of technology transfer, this article explores processes of domestication (kokusanka) using the records of the Japan Penicillin Research Association (Nihon penishirin gakujutsu kyōgikai), an interdisciplinary academic association set up to mediate between government policy and industrial manufacturers, and which directed research in the critical early years of penicillin production. I argue that an examination of the occupation period is especially revealing of the contribution of indigenous knowledge from the World War II and prewar periods to the development of microbiology during Japan’s “economic miracle” (1950s to early 1970s), and I highlight the intellectual dimensions that were specific to Japanese science by comparison with other national cases of penicillin domestication. Beyond the transfer of submerged culture fermentation technology for antibiotic mass production, a distinctive engagement with agricultural chemistry’s longstanding perception of microbes—as alchemists of the environment, with the ability to transform resource scarcity into productive abundance—organized the knowledge by which penicillin scientists made the domestic environment work, and deeply shaped antibiotic research in the subsequent decades in Japan.

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Kolchyk, O. V., Т. R. Levytskyi, A. І. Buzun, E. Çelik, D. M. Hrynchenko, І. V. Korovin, and Yu V. Orda. "Microbial biofilms and microbial contamination of feed for livestock animals: Challenges and ways to overcome them." Journal for Veterinary Medicine, Biotechnology and Biosafety 7, no. 4 (December 23, 2021): 31–35. http://dx.doi.org/10.36016/jvmbbs-2021-7-4-6.

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The article describes the problem of microbial contamination of feed in animal husbandry and the microflora that causes mastitis in lactating cows. The microbial contamination of 52 commercial batches of fodder from 5 farms of 3 regions of Ukraine (barley, corn silage, oat haylage, alfalfa hay, sunflower meal) has been determined. Pasteurella multocida in association with Neisseria lactamica, Actinobacillus pleuropneumonia, Clostridium perfringens was isolated from 61.5% of barley, 66.7% of corn silage, 60.0% of alfalfa hay, and 50.0% of sunflower meal. 262 samples of milk from cows with mastitis have been studied. Aspergillus candidus, Aspergillus niger were most often isolated in association with Mycoplasma bovis, Streptococcus agalactiae, Candida albicans, Neisseria sicca, Clostridium perfringens. High film-forming activity of microorganisms in feed was determined, by optical density: Pasteurella multocida + Actinobacillus pleuropneumonia D620 = 3.76 and Pasteurella multocida, Actinobacillus pleuropneumonia, Neisseria lactamica D620 = 3.62. While from the milk of cows with mastitis we isolated associations of microorganisms that were strong producers of biofilms by the optical densities D620 = 4.02 and 4.23

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Liu, Fei, Shao-Wu Zhang, Ze-Gang Wei, Wei Chen, and Chen Zhou. "Mining Seasonal Marine Microbial Pattern with Greedy Heuristic Clustering and Symmetrical Nonnegative Matrix Factorization." BioMed Research International 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/189590.

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With the development of high-throughput and low-cost sequencing technology, a large number of marine microbial sequences were generated. The association patterns between marine microbial species and environment factors are hidden in these large amount sequences. Mining these association patterns is beneficial to exploit the marine resources. However, very few marine microbial association patterns are well investigated in this field. The present study reports the development of a novel method called HC-sNMF to detect the marine microbial association patterns. The results show that the four seasonal marine microbial association networks have characters of complex networks, the same environmental factor influences different species in the four seasons, and the correlative relationships are stronger between OTUs (taxa) than with environmental factors in the four seasons detecting community.

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Orlova, Ekaterina, Tom Dudding, Jonathan M. Chernus, Rasha N. Alotaibi, Simon Haworth, Richard J. Crout, Myoung Keun Lee, et al. "Association of Early Childhood Caries with Bitter Taste Receptors: A Meta-Analysis of Genome-Wide Association Studies and Transcriptome-Wide Association Study." Genes 14, no. 1 (December 24, 2022): 59. http://dx.doi.org/10.3390/genes14010059.

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Although genetics affects early childhood caries (ECC) risk, few studies have focused on finding its specific genetic determinants. Here, we performed genome-wide association studies (GWAS) in five cohorts of children (aged up to 5 years, total N = 2974, cohorts: Center for Oral Health Research in Appalachia cohorts one and two [COHRA1, COHRA2], Iowa Fluoride Study, Iowa Head Start, Avon Longitudinal Study of Parents and Children [ALSPAC]) aiming to identify genes with potential roles in ECC biology. We meta-analyzed the GWASs testing ~3.9 million genetic variants and found suggestive evidence for association at genetic regions previously associated with caries in primary and permanent dentition, including the β-defensin anti-microbial proteins. We then integrated the meta-analysis results with gene expression data in a transcriptome-wide association study (TWAS). This approach identified four genes whose genetically predicted expression was associated with ECC (p-values < 3.09 × 10−6; CDH17, TAS2R43, SMIM10L1, TAS2R14). Some of the strongest associations were with genes encoding members of the bitter taste receptor family (TAS2R); other members of this family have previously been associated with caries. Of note, we identified the receptor encoded by TAS2R14, which stimulates innate immunity and anti-microbial defense in response to molecules released by the cariogenic bacteria, Streptococcus mutans and Staphylococcus aureus. These findings provide insight into ECC genetic architecture, underscore the importance of host-microbial interaction in caries risk, and identify novel risk genes.

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Saikia, Surjya, Sudarshana Nandi, and Sandip Majumder. "‘Synbiofilm’- A Friendly Microbial Association in Aquatic Ecosystem." Annual Research & Review in Biology 5, no. 2 (January 10, 2015): 97–108. http://dx.doi.org/10.9734/arrb/2015/10368.

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Perdek, Joyce M., and Michael Borst. "MICROBIAL PARTICLE ASSOCIATION AND COMBINED SEWER OVERFLOW DISINFECTION." Proceedings of the Water Environment Federation 2000, no. 2 (January 1, 2000): 329–47. http://dx.doi.org/10.2175/193864700785371948.

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Wierinck, Isabella, and Willy Verstraete. "Degradation of atrazine by a hydrogenotrophic microbial association." Environmental Technology 11, no. 9 (September 1990): 843–52. http://dx.doi.org/10.1080/09593339009384932.

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13

MacDonald, Norman J., and Robert G. Beiko. "Efficient learning of microbial genotype–phenotype association rules." Bioinformatics 26, no. 15 (June 6, 2010): 1834–40. http://dx.doi.org/10.1093/bioinformatics/btq305.

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Faust, Karoline, and Jeroen Raes. "CoNet app: inference of biological association networks using Cytoscape." F1000Research 5 (June 27, 2016): 1519. http://dx.doi.org/10.12688/f1000research.9050.1.

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Here we present the Cytoscape app version of our association network inference tool CoNet. Though CoNet was developed with microbial community data from sequencing experiments in mind, it is designed to be generic and can detect associations in any data set where biological entities (such as genes, metabolites or species) have been observed repeatedly. The CoNet app supports Cytoscape 2.x and 3.x and offers a variety of network inference approaches, which can also be combined. Here we briefly describe its main features and illustrate its use on microbial count data obtained by 16S rDNA sequencing of arctic soil samples. The CoNet app is available at: http://apps.cytoscape.org/apps/conet.

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Faust, Karoline, and Jeroen Raes. "CoNet app: inference of biological association networks using Cytoscape." F1000Research 5 (October 14, 2016): 1519. http://dx.doi.org/10.12688/f1000research.9050.2.

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Here we present the Cytoscape app version of our association network inference tool CoNet. Though CoNet was developed with microbial community data from sequencing experiments in mind, it is designed to be generic and can detect associations in any data set where biological entities (such as genes, metabolites or species) have been observed repeatedly. The CoNet app supports Cytoscape 2.x and 3.x and offers a variety of network inference approaches, which can also be combined. Here we briefly describe its main features and illustrate its use on microbial count data obtained by 16S rDNA sequencing of arctic soil samples. The CoNet app is available at: http://apps.cytoscape.org/apps/conet.

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Ghosh, Asit Ranjan. "Appraisal of Microbial Evolution to Commensalism and Pathogenicity in Humans." Clinical Medicine Insights: Gastroenterology 6 (January 2013): CGast.S11858. http://dx.doi.org/10.4137/cgast.s11858.

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The human body is host to a number of microbes occurring in various forms of host-microbe associations, such as commensals, mutualists, pathogens and opportunistic symbionts. While this association with microbes in certain cases is beneficial to the host, in many other cases it seems to offer no evident benefit or motive. The emergence and re-emergence of newer varieties of infectious diseases with causative agents being strains that were once living in the human system makes it necessary to study the environment and the dynamics under which this host microbe relationship thrives. The present discussion examines this interaction while tracing the origins of this association, and attempts to hypothesize a possible framework of selective pressures that could have lead microbes to inhabit mammalian host systems.

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Shilo, Smadar, Anastasia Godneva, Marianna Rachmiel, Tal Korem, Yuval Bussi, Dmitry Kolobkov, Tal Karady, et al. "The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control." Diabetes Care 45, no. 3 (January 19, 2022): 555–63. http://dx.doi.org/10.2337/dc21-1656.

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OBJECTIVE Previous studies have demonstrated an association between gut microbiota composition and type 1 diabetes (T1D) pathogenesis. However, little is known about the composition and function of the gut microbiome in adults with longstanding T1D or its association with host glycemic control. RESEARCH DESIGN AND METHODS We performed a metagenomic analysis of the gut microbiome obtained from fecal samples of 74 adults with T1D, 14.6 ± 9.6 years following diagnosis, and compared their microbial composition and function to 296 age-matched healthy control subjects (1:4 ratio). We further analyzed the association between microbial taxa and indices of glycemic control derived from continuous glucose monitoring measurements and blood tests and constructed a prediction model that solely takes microbiome features as input to evaluate the discriminative power of microbial composition for distinguishing individuals with T1D from control subjects. RESULTS Adults with T1D had a distinct microbial signature that separated them from control subjects when using prediction algorithms on held-out subjects (area under the receiver operating characteristic curve = 0.89 ± 0.03). Linear discriminant analysis showed several bacterial species with significantly higher scores in T1D, including Prevotella copri and Eubacterium siraeum, and species with higher scores in control subjects, including Firmicutes bacterium and Faecalibacterium prausnitzii (P < 0.05, false discovery rate corrected for all). On the functional level, several metabolic pathways were significantly lower in adults with T1D. Several bacterial taxa and metabolic pathways were associated with the host’s glycemic control. CONCLUSIONS We identified a distinct gut microbial signature in adults with longstanding T1D and associations between microbial taxa, metabolic pathways, and glycemic control indices. Additional mechanistic studies are needed to identify the role of these bacteria for potential therapeutic strategies.

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Shi, W., J. Becker, M. Bischoff, R. F. Turco, and A. E. Konopka. "Association of Microbial Community Composition and Activity with Lead, Chromium, and Hydrocarbon Contamination." Applied and Environmental Microbiology 68, no. 8 (August 2002): 3859–66. http://dx.doi.org/10.1128/aem.68.8.3859-3866.2002.

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ABSTRACT Microbial community composition and activity were characterized in soil contaminated with lead (Pb), chromium (Cr), and hydrocarbons. Contaminant levels were very heterogeneous and ranged from 50 to 16,700 mg of total petroleum hydrocarbons (TPH) kg of soil−1, 3 to 3,300 mg of total Cr kg of soil−1, and 1 to 17,100 mg of Pb kg of soil−1. Microbial community compositions were estimated from the patterns of phospholipid fatty acids (PLFA); these were considerably different among the 14 soil samples. Statistical analyses suggested that the variation in PLFA was more correlated with soil hydrocarbons than with the levels of Cr and Pb. The metal sensitivity of the microbial community was determined by extracting bacteria from soil and measuring [3H]leucine incorporation as a function of metal concentration. Six soil samples collected in the spring of 1999 had IC50 values (the heavy metal concentrations giving 50% reduction of microbial activity) of approximately 2.5 mM for CrO4 2− and 0.01 mM for Pb2+. Much higher levels of Pb were required to inhibit [14C]glucose mineralization directly in soils. In microcosm experiments with these samples, microbial biomass and the ratio of microbial biomass to soil organic C were not correlated with the concentrations of hydrocarbons and heavy metals. However, microbial C respiration in samples with a higher level of hydrocarbons differed from the other soils no matter whether complex organic C (alfalfa) was added or not. The ratios of microbial C respiration to microbial biomass differed significantly among the soil samples (P < 0.05) and were relatively high in soils contaminated with hydrocarbons or heavy metals. Our results suggest that the soil microbial community was predominantly affected by hydrocarbons.

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Karaulov, A. V., M. S. Afanasiev, Yu V. Nesvizhsky, S. S. Afanasiev, E. A. Voropaeva, O. Yu Borisova, A. D. Voropaev, and A. B. Borisova. "Microbial pathogens in urogenital infection in pregnant women." Journal of microbiology epidemiology immunobiology, no. 6 (December 16, 2019): 13–20. http://dx.doi.org/10.36233/0372-9311-2019-6-13-20.

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Introduction. Chronic and latent infections are often activated during pregnancy.Aim - to asses the pathogenetic role of microbial pathogens in urogenital tract infection (UTI) in pregnant women.Materials and methods. 89 pregnant women underwent general clinical examination, examination of smears from urethra, vagina, cervical canal; bacteriological analysis of vaginal contents; enzyme-linked immunosorbent assay, polymerase chain reaction and determination of specific antibodies for verification of herpes simplex virus (HSV) type I and II, cytomegalovirus (CMV), Epstein-Barr (EBV) and UTI pathogens in pregnant women in blood and mucosal scrapes.Results. Prevalence of Herpesviridae was revealed (90-100% -EBV, HSV type I and II, CMV); in 41% of cases - bacterial pathogens, in 57% of cases - Mycoplasma, Ureaplasma.Discussion. In preterm birth and pregnancy termination mycoplasma and ureaplasma were more often revealed, and in pregnancy termination - association of HSV type I and II in comparison with urgent birth; in the last equally often - HSV type I and association of HSV type I and II; in urgent birth (infection) more often - HSV type I, than association of HSV type I and II; in preterm birth more often - HSV type I, than the association of HSV types I and II, and less often than combination of HSV type I and association of HSV types I and II in pregnancy termination; in the last, the association of HSV types I and II is more common than HSV type I. Increase of TLRs genes expression levels depends on HSV type I less than from association of HSV types I and II, less than from combination of HSV type I and association of HSV types I and II (it determines the clinical manifestations of genital herpes).Conclusion. Microbial pathogens determine the character of pregnancy course, and HSV types I and II- are the triggers of the infectious process, prognosing its course.

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Cheng, Liang, Changlu Qi, He Zhuang, Tongze Fu, and Xue Zhang. "gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions." Nucleic Acids Research 48, no. D1 (October 4, 2019): D554—D560. http://dx.doi.org/10.1093/nar/gkz843.

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Abstract gutMDisorder (http://bio-annotation.cn/gutMDisorder), a manually curated database, aims at providing a comprehensive resource of dysbiosis of the gut microbiota in disorders and interventions. Alterations in the composition of the gut microbial community play crucial roles in the development of chronic disorders. And the beneficial effects of drugs, foods and other intervention measures on disorders could be microbially mediated. The current version of gutMDisorder documents 2263 curated associations between 579 gut microbes and 123 disorders or 77 intervention measures in Human, and 930 curated associations between 273 gut microbes and 33 disorders or 151 intervention measures in Mouse. Each entry in the gutMDisorder contains detailed information on an association, including an intestinal microbe, a disorder name, intervention measures, experimental technology and platform, characteristic of samples, web sites for downloading the sequencing data, a brief description of the association, a literature reference, and so on. gutMDisorder provides a user-friendly interface to browse, retrieve each entry using gut microbes, disorders, and intervention measures. It also offers pages for downloading all the entries and submitting new experimentally validated associations.

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Hertel, Johannes, Daniel Fässler, Almut Heinken, Frank Weiß, Malte Rühlemann, Corinna Bang, Andre Franke, et al. "NMR Metabolomics Reveal Urine Markers of Microbiome Diversity and Identify Benzoate Metabolism as a Mediator between High Microbial Alpha Diversity and Metabolic Health." Metabolites 12, no. 4 (March 31, 2022): 308. http://dx.doi.org/10.3390/metabo12040308.

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Microbial metabolites measured using NMR may serve as markers for physiological or pathological host–microbe interactions and possibly mediate the beneficial effects of microbiome diversity. Yet, comprehensive analyses of gut microbiome data and the urine NMR metabolome from large general population cohorts are missing. Here, we report the associations between gut microbiota abundances or metrics of alpha diversity, quantified from stool samples using 16S rRNA gene sequencing, with targeted urine NMR metabolites measures from 951 participants of the Study of Health in Pomerania (SHIP). We detected significant genus–metabolite associations for hippurate, succinate, indoxyl sulfate, and formate. Moreover, while replicating the previously reported association between hippurate and measures of alpha diversity, we identified formate and 4-hydroxyphenylacetate as novel markers of gut microbiome alpha diversity. Next, we predicted the urinary concentrations of each metabolite using genus abundances via an elastic net regression methodology. We found profound associations of the microbiome-based hippurate prediction score with markers of liver injury, inflammation, and metabolic health. Moreover, the microbiome-based prediction score for hippurate completely mediated the clinical association pattern of microbial diversity, hinting at a role of benzoate metabolism underlying the positive associations between high alpha diversity and healthy states. In conclusion, large-scale NMR urine metabolomics delivered novel insights into metabolic host–microbiome interactions, identifying pathways of benzoate metabolism as relevant candidates mediating the beneficial health effects of high microbial alpha diversity.

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Ishaq, Hafiz Muhammad, Imran Shair Mohammad, Kiran Sher Muhammad, Huan Li, Rao Zahid Abbas, Zia ud Din Sindhu, Shakir Ullah, et al. "Gut microbial dysbiosis and its association with esophageal cancer." Journal of Applied Biomedicine 19, no. 1 (March 3, 2021): 1–13. http://dx.doi.org/10.32725/jab.2021.005.

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Donnelly, Catherine W. "Concerns of Microbial Pathogens in Association with Dairy Foods." Journal of Dairy Science 73, no. 6 (June 1990): 1656–61. http://dx.doi.org/10.3168/jds.s0022-0302(90)78838-8.

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Gardner, A., P. W. So, and G. H. Carpenter. "Intraoral Microbial Metabolism and Association with Host Taste Perception." Journal of Dental Research 99, no. 6 (May 20, 2020): 739–45. http://dx.doi.org/10.1177/0022034520917142.

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Metabolomics has been identified as a means of functionally assessing the net biological activity of a particular microbial community. Considering the oral microbiome, such an approach remains largely underused. While the current knowledge of the oral microbiome is constantly expanding, there are several deficits in knowledge particularly relating to their interactions with their host. This work uses nuclear magnetic resonance spectroscopy to investigate metabolic differences between oral microbial metabolism of endogenous (i.e., salivary protein) and exogenous (i.e., dietary carbohydrates) substrates. It also investigated whether microbial generation of different metabolites may be associated with host taste perception. This work found that in the absence of exogenous substrate, oral bacteria readily catabolize salivary protein and generate metabolic profiles similar to those seen in vivo. Important metabolites such as acetate, butyrate, and propionate are generated at relatively high concentrations. Higher concentrations of metabolites were generated by tongue biofilm compared to planktonic salivary bacteria. Thus, as has been postulated, metabolite production in proximity to taste receptors could reach relatively high concentrations. In the presence of 0.25 M exogenous sucrose, increased catabolism was observed with increased concentrations of a range of metabolites relating to glycolysis (lactate, pyruvate, succinate). Additional pyruvate-derived molecules such as acetoin and alanine were also increased. Furthermore, there was evidence that individual taste sensitivity to sucrose was related to differences in the metabolic fate of sucrose in the mouth. High-sensitivity perceivers appeared more inclined toward continual citric acid cycle activity postsucrose, whereas low-sensitivity perceivers had a more efficient conversion of pyruvate to lactate. This work collectively indicates that the oral microbiome exists in a complex balance with the host, with fluctuating metabolic activity depending on nutrient availability. There is preliminary evidence of an association between host behavior (sweet taste perception) and oral catabolism of sugar.

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Dobra, Adrian, Camilo Valdes, Dragana Ajdic, Bertrand Clarke, and Jennifer Clarke. "Modeling association in microbial communities with clique loglinear models." Annals of Applied Statistics 13, no. 2 (June 2019): 931–57. http://dx.doi.org/10.1214/18-aoas1229.

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Power, Robert A., Julian Parkhill, and Tulio de Oliveira. "Microbial genome-wide association studies: lessons from human GWAS." Nature Reviews Genetics 18, no. 1 (November 14, 2016): 41–50. http://dx.doi.org/10.1038/nrg.2016.132.

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Kiran, G. Seghal, Sivasankari Sekar, Pasiyappazham Ramasamy, Thangadurai Thinesh, Saqib Hassan, Anuj Nishanth Lipton, A. S. Ninawe, and Joseph Selvin. "Marine sponge microbial association: Towards disclosing unique symbiotic interactions." Marine Environmental Research 140 (September 2018): 169–79. http://dx.doi.org/10.1016/j.marenvres.2018.04.017.

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Quinn, P. A., J. Butany, J. Taylor, and W. Hannah. "Chorioamnionitis: Its association with pregnancy outcome and microbial infection." American Journal of Obstetrics and Gynecology 156, no. 2 (February 1987): 379–87. http://dx.doi.org/10.1016/0002-9378(87)90288-2.

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Creamer, Courtney A., Andrea L. Foster, Corey Lawrence, Jack McFarland, Marjorie Schulz, and Mark P. Waldrop. "Mineralogy dictates the initial mechanism of microbial necromass association." Geochimica et Cosmochimica Acta 260 (September 2019): 161–76. http://dx.doi.org/10.1016/j.gca.2019.06.028.

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Tamura, Makio, and Patrik D'haeseleer. "Microbial genotype–phenotype mapping by class association rule mining." Bioinformatics 24, no. 13 (May 8, 2008): 1523–29. http://dx.doi.org/10.1093/bioinformatics/btn210.

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Quinn, PA, J. Butany, J. Taylor, and W. Hannah. "Chorioamnionitis: Its association with pregnancy outcome and microbial infection." International Journal of Gynecology & Obstetrics 26, no. 1 (February 1988): 169. http://dx.doi.org/10.1016/0020-7292(88)90250-0.

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Vasilevskaya, L. A. "The microbial landscape action on development destructive erysipelas forms." Modern medical technologies 41 part 1, no. 2 (April 6, 2019): 17–19. http://dx.doi.org/10.34287/mmt.2(41).2019.3.

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Objective. Changes in the monoculture of the pathogen in the microbial association of bacterial pathogens is accompanied, depending on their species composition, the progression of the inflammatory process with the development of destructive forms. The object was to install the value of microbial landscape in predicting the development of destructive forms of erysipelas. Material and methods. The diseases histories and cultures of wound secretions with the definition of sensitivity of microorganisms to antibiotics were analyses. Results. Of our studies indicate that the microflora of the primary cells in destructive forms of the erysipelas changed both quantitatively and qualitatively. Detected microbial pathogens in bacteriological studies of soft tissue exudates allowed installing criteria for forecasting the development of purulent complications. Conclusion. Bacteriological studies indicate that necrotizing skin lesions are preceded by the presence of S. Pyogenes in the exudates. Keywords: microbial landscape, erysipelas, gram-positive and gram-negative microflora, microbial associations.

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Bourillot, Raphaël, Emmanuelle Vennin, Christophe Dupraz, Aurélie Pace, Anneleen Foubert, Jean-Marie Rouchy, Patricia Patrier, et al. "The Record of Environmental and Microbial Signatures in Ancient Microbialites: The Terminal Carbonate Complex from the Neogene Basins of Southeastern Spain." Minerals 10, no. 3 (March 19, 2020): 276. http://dx.doi.org/10.3390/min10030276.

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The Messinian microbialites of the Terminal Carbonate Complex (TCC) from the Neogene basins of southeastern Spain show both diversified morphologies and an excellent preservation of primary microbial microstructures. Their stratigraphic architecture, fabric (micro-, meso-, and macro-fabric), and mineralogical composition were investigated in eight localities from three sedimentary basins of southeastern Spain: The Sorbas and Bajo Segura basins and the Agua Amarga depression. Two recurrent microbialite associations were distinguished. Laterally linked low relief stromatolites predominated in Microbialite Association 1 (MA1), which probably formed in low energy lagoons or lakes with fluctuating normal marine to hypersaline water. The microfabrics of MA1 reflected the predominance of microbially induced/influenced precipitation of carbonates and locally (Ca)-Mg-Al silicates. Microbialite Association 2 (MA2) developed in high energy wave and tidal influenced foreshore to shoreface, in normal marine to hypersaline water. High-relief buildups surrounded by mobile sediment (e.g., ooids or pellets) dominated in this environment. MA2 microbialites showed a significant proportion of thrombolitic mesofabric. Grain-rich microfabrics indicated that trapping and binding played a significant role in their accretion, together with microbially induced/influenced carbonate precipitation. The stratigraphic distribution of MA1 and MA2 was strongly influenced by water level changes, the morphology and nature of the substratum, and exposure to waves. MA1 favorably developed in protected areas during third to fourth order early transgression and regression phases. MA2 mostly formed during the late transgressions and early regressions in high energy coastal areas, often corresponding to fossil coral reefs. Platform scale syn-sedimentary gypsum deformation and dissolution enhanced microbial carbonate production, microbialites being thicker and more extended in zones of maximum deformation/dissolution. Microbial microstructures (e.g., microbial peloids) and microfossils were preserved in the microbialites. Dolomite microspheres and filaments showed many morphological similarities with some of the cyanobacteria observed in modern open marine and hypersaline microbialites. Dolomite potentially replaced a metastable carbonate phase during early diagenesis, possibly in close relationship with extracellular polymeric substances (EPS) degradation. Double-layered microspheres locally showed an inner coating made of (Ca)-Mg-Al silicates and carbonates. This mineral coating could have formed around coccoid cyanobacteria and indicated an elevated pH in the upper part of the microbial mats and a potential dissolution of diatoms as a source of silica. Massive primary dolomite production in TCC microbialites may have resulted from enhanced sulfate reduction possibly linked to the dissolving gypsum that would have provided large amounts of sulfate-rich brines to microbial mats. Our results open new perspectives for the interpretation of ancient microbialites associated with major evaporite deposits, from microbe to carbonate platform scales.

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Tal, Ofir, Rotem Bartuv, Maria Vetcos, Shlomit Medina, Jiandong Jiang, and Shiri Freilich. "NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data." Microorganisms 9, no. 9 (August 30, 2021): 1838. http://dx.doi.org/10.3390/microorganisms9091838.

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The study of microbial activity can be viewed as a triangle with three sides: environment (dominant resources in a specific habitat), community (species dictating a repertoire of metabolic conversions) and function (production and/or utilization of resources and compounds). Advances in metagenomics enable a high-resolution description of complex microbial communities in their natural environments and support a systematic study of environment-community-function associations. NetCom is a web-tool for predicting metabolic activities of microbial communities based on network-based interpretation of assembled and annotated metagenomics data. The algorithm takes as an input, lists of differentially abundant enzymatic reactions and generates the following outputs: (i) pathway associations of differently abundant enzymes; (ii) prediction of environmental resources that are unique to each treatment, and their pathway associations; (iii) prediction of compounds that are produced by the microbial community, and pathway association of compounds that are treatment-specific; (iv) network visualization of enzymes, environmental resources and produced compounds, that are treatment specific (2 and 3D). The tool is demonstrated on metagenomic data from rhizosphere and bulk soil samples. By predicting root-specific activities, we illustrate the relevance of our framework for forecasting the impact of soil amendments on the corresponding microbial communities. NetCom is available online.

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Pekkanen, Juha, Maria Valkonen, Martin Täubel, Christina Tischer, Hanna Leppänen, Päivi M. Kärkkäinen, Helena Rintala, et al. "Indoor bacteria and asthma in adults: a multicentre case–control study within ECRHS II." European Respiratory Journal 51, no. 2 (February 2018): 1701241. http://dx.doi.org/10.1183/13993003.01241-2017.

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Both protective and adverse effects of indoor microbial exposure on asthma have been reported, but mostly in children. To date, no study in adults has used non-targeted methods for detection of indoor bacteria followed by quantitative confirmation.A cross-sectional study of 198 asthmatic and 199 controls was conducted within the European Community Respiratory Health Survey (ECRHS) II. DNA was extracted from mattress dust for bacterial analysis using denaturing gradient gel electrophoresis (DGGE). Selected bands were sequenced and associations with asthma confirmed with four quantitative PCR (qPCR) assays.15 out of 37 bands detected with DGGE, which had at least a suggestive association (p<0.25) with asthma, were sequenced. Of the four targeted qPCRs,Clostridiumcluster XI confirmed the protective association with asthma. The association was dose dependent (aOR 0.43 (95% CI 0.22–0.84) for the fourthversusfirst quartile, p for trend 0.009) and independent of other microbial markers. Few significant associations were observed for the three other qPCRs used.In this large international study, the level ofClostridiumcluster XI was independently associated with a lower risk of prevalent asthma. Results suggest the importance of environmental bacteria also in adult asthma, but need to be confirmed in future studies.

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MOURA, ALEXANDRE C. DE, SILVIO C. SAMPAIO, MARCELO B. REMOR, ADRIANA P. DA SILVA, and PAMELA A. M. PEREIRA. "LONG-TERM EFFECTS OF SWINE wastewater AND MINERAL FERTILIZER ASSOCIATION ON SOIL MICROBIOTA." Engenharia Agrícola 36, no. 2 (April 2016): 318–28. http://dx.doi.org/10.1590/1809-4430-eng.agric.v36n2p318-328/2016.

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ABSTRACT Swine wastewater (SW) application in agricultural soils may affect its microbial community in a long term. The objective of this study was to evaluate prospective changes in soil bacterial community after eight years continuous application of swine wastewater. The wastewater doses tested were 0; 100; 200 and 300 m3 ha-1, being applied from the beginning of the experiment and with or without recommended fertilization. Three soil samples were taken from each plot for determinations of basal respiration, microbial biomass and metabolic quotient. We also performed DGGE analysis and made a correlation between soil chemical conditions and microbial activity. Microbial community underwent significant structural changes from swine wastewater applications. Higher SW doses (200 and 300 m3 ha-1) influenced significantly (p <0.05) and benefitted certain bacteria groups.

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Zhou, Jingya, Shouyi Yin, Qionglin Fu, Qingqing Wang, Qing Huang, and Junfeng Wang. "Microbial-induced concrete corrosion under high-salt conditions: Microbial community composition and environmental multivariate association analysis." International Biodeterioration & Biodegradation 164 (October 2021): 105287. http://dx.doi.org/10.1016/j.ibiod.2021.105287.

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Mallick, Himel, Ali Rahnavard, Lauren J. McIver, Siyuan Ma, Yancong Zhang, Long H. Nguyen, Timothy L. Tickle, et al. "Multivariable association discovery in population-scale meta-omics studies." PLOS Computational Biology 17, no. 11 (November 16, 2021): e1009442. http://dx.doi.org/10.1371/journal.pcbi.1009442.

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It is challenging to associate features such as human health outcomes, diet, environmental conditions, or other metadata to microbial community measurements, due in part to their quantitative properties. Microbiome multi-omics are typically noisy, sparse (zero-inflated), high-dimensional, extremely non-normal, and often in the form of count or compositional measurements. Here we introduce an optimized combination of novel and established methodology to assess multivariable association of microbial community features with complex metadata in population-scale observational studies. Our approach, MaAsLin 2 (Microbiome Multivariable Associations with Linear Models), uses generalized linear and mixed models to accommodate a wide variety of modern epidemiological studies, including cross-sectional and longitudinal designs, as well as a variety of data types (e.g., counts and relative abundances) with or without covariates and repeated measurements. To construct this method, we conducted a large-scale evaluation of a broad range of scenarios under which straightforward identification of meta-omics associations can be challenging. These simulation studies reveal that MaAsLin 2’s linear model preserves statistical power in the presence of repeated measures and multiple covariates, while accounting for the nuances of meta-omics features and controlling false discovery. We also applied MaAsLin 2 to a microbial multi-omics dataset from the Integrative Human Microbiome (HMP2) project which, in addition to reproducing established results, revealed a unique, integrated landscape of inflammatory bowel diseases (IBD) across multiple time points and omics profiles.

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Palmu, Joonatan, Leo Lahti, and Teemu Niiranen. "Targeting Gut Microbiota to Treat Hypertension: A Systematic Review." International Journal of Environmental Research and Public Health 18, no. 3 (January 30, 2021): 1248. http://dx.doi.org/10.3390/ijerph18031248.

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While hypertension remains the leading modifiable risk factor for cardiovascular morbidity and mortality, the pathogenesis of essential hypertension remains only partially understood. Recently, microbial dysbiosis has been associated with multiple chronic diseases closely related to hypertension. In addition, multiple small-scale animal and human studies have provided promising results for the association between gut microbial dysbiosis and hypertension. Animal models and a small human pilot study, have demonstrated that high salt intake, a risk factor for both hypertension and cardiovascular disease, depletes certain Lactobacillus species while oral treatment of Lactobacilli prevented salt-sensitive hypertension. To date, four large cohort studies have reported modest associations between gut microbiota features and hypertension. In this systematic literature review, we examine the previously reported links between the gut microbiota and hypertension and what is known about the functional mechanisms behind this association.

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Sharifullina, D. M., R. M. Vasil’eva, T. I. Yakovleva, E. G. Nikolaeva, O. K. Pozdeev, A. P. Lozhkin, and R. N. Khayrullin. "Microbial landscape of atherosclerotic plaques biopsy samples." Kazan medical journal 96, no. 6 (December 15, 2015): 979–82. http://dx.doi.org/10.17750/kmj2015-979.

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Aim. To study the microflora composition of different localization atherosclerotic plaques in patients with atherosclerosis. Methods. 88 samples of atherosclerotic plaques were analyzed, including brachycephalic arteries - 71, the coronary arteries - 13, the aorta - 2, vessels of lower extremities - 2. The specimens were obtained from 71 men and 17 women aged 30-79 years (mean age 50.8 years). The presence of aerobic and anaerobic microflora was determined by bacteriological method. Detection of the cytomegalovirus nucleic acid, herpes simplex virus types 1 and 2, Epstein-Barr virus was performed by real time polymerase chain reaction. Results. The most diverse microflora was represented in the plaques of the neck vessels (carotid arteries). Thereat we found bacteria in 77.5% of the samples, including Propionibacterium acnes - 40.8%, the Staphylococcus genus - 50.7%. 83.3% Staphylococcus isolates were identified as S. epidermidis. In 14.1% of the samples from the brachycephalic artery plaques microorganisms associations (P. acnes and S. epidermidis) were found. The coronary arteries and aorta plaques microflora was represented entirely by P. acnes - 15.4 and 50% respectively. Herpes simplex virus type 1 and 2, and Epstein-Barr virus nucleic acids were detected in 6.7% of samples of carotid artery atherosclerotic plaques. Bacteria associations were presented exclusively in atherosclerotic plaques from brachycephalic arteries - 11.4% of the samples, including 9 bacteria (P. acnes and S. epidermidis) associations, and one association consisted of 3 microorganisms: 2 bacteria (P. acnes and S. epidermidis) and the virus (Epstein-Barr virus). Conclusion. Observed high frequency of microorganisms detection in studied atherosclerotic plaques samples allows to suggest their possible pathogenetic role in the blood vessels endothelium atherosclerotic lesions formation.

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Szabo, Helga, Anita Hernyes, Marton Piroska, Balazs Ligeti, Peter Fussy, Luca Zoldi, Szonja Galyasz, et al. "Association between Gut Microbial Diversity and Carotid Intima-Media Thickness." Medicina 57, no. 3 (February 25, 2021): 195. http://dx.doi.org/10.3390/medicina57030195.

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Background and Objectives: There is an increasing focus on the effect of the gut microbiome on developing atherosclerosis, but there is still no unified standpoint. We aimed to find associations between intestinal microbiome diversity and a marker of subclinical atherosclerosis, the carotid intima-media thickness (IMT). Materials and Methods: Recruited from the Hungarian Twin Registry, 108 monozygotic (MZ) twins (mean age 52.4 ± 14.1 years, 58% female) underwent a comprehensive carotid ultrasound examination (Samsung RS85). Of the 108 MZ twins, 14 pairs (mean age 65 ± 6.4 years, 71% female) discordant for carotid IMT were selected to undergo a stool sample collection. A special stool sampling container was mailed and received from each participant. After DNA extraction, library construction was performed specifically for the V3–V4 hypervariable region of microbial 16S rRNA. Next, the microbiome composition of the samples was determined using Kraken software. Two hypotheses were tested with the exact permutation test: (1) in the group with normal IMT, the Shannon index of the phyla is higher; and (2) the Firmicutes/Bacteroidetes ratio is greater in the group with high IMT values. Furthermore, the abundance of different bacterial strains present at higher and normal IMT was also explored. Statistical analysis was carried out using R software. Results: Increased Firmicutes/Bacteroidetes ratio was associated with increased IMT (mean Firmicutes/Bacteroidetes ratio of IMT > 0.9 and IMT < 0.9 groups: 2.299 and 1.436, respectively; p = 0.031). In the group with normal IMT values, a substantially higher fraction of Prevotellaceae was observed in contrast with subjects having subclinical atherosclerosis. However, there was no significant difference in the alpha diversity between the two groups. Conclusions: The determining role of individual genera and their proportions in the development and progression of atherosclerosis can be assumed. Further studies are needed to clarify if these findings can be used as potential therapeutic targets.

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Khan, Rehana, Abhishek Sharma, Raghul Ravikumar, Avani Parekh, Ramyaa Srinivasan, Ronnie Jacob George, and Rajiv Raman. "Association Between Gut Microbial Abundance and Sight-Threatening Diabetic Retinopathy." Investigative Opthalmology & Visual Science 62, no. 7 (June 16, 2021): 19. http://dx.doi.org/10.1167/iovs.62.7.19.

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Gingras, Murray, James W. Hagadorn, Adolf Seilacher, Stefan V. Lalonde, Ernesto Pecoits, Daniel Petrash, and Kurt O. Konhauser. "Possible evolution of mobile animals in association with microbial mats." Nature Geoscience 4, no. 6 (May 15, 2011): 372–75. http://dx.doi.org/10.1038/ngeo1142.

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Gilbert, Jack A., Robert A. Quinn, Justine Debelius, Zhenjiang Z. Xu, James Morton, Neha Garg, Janet K. Jansson, Pieter C. Dorrestein, and Rob Knight. "Microbiome-wide association studies link dynamic microbial consortia to disease." Nature 535, no. 7610 (July 2016): 94–103. http://dx.doi.org/10.1038/nature18850.

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Lees, John A., Marco Galardini, Stephen D. Bentley, Jeffrey N. Weiser, and Jukka Corander. "pyseer: a comprehensive tool for microbial pangenome-wide association studies." Bioinformatics 34, no. 24 (July 2, 2018): 4310–12. http://dx.doi.org/10.1093/bioinformatics/bty539.

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Taylor, Kent D., Talin Haritunians, Dermot P. McGovern, Carol J. Landers, Andrew Ippoliti, Eric A. Vasiliauskas, Xiuqing Guo, Marla Dubinsky, Stephan R. Targan, and Jerome I. Rotter. "Genome-Wide Association Study of CD-Associated Anti-Microbial Antibodies." Gastroenterology 140, no. 5 (May 2011): S—271. http://dx.doi.org/10.1016/s0016-5085(11)61084-6.

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Volkmann, Elizabeth R., Yu-Ling Chang, Nashla Barroso, Daniel E. Furst, Philip J. Clements, Alan H. Gorn, Bennett E. Roth, et al. "Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium." Arthritis & Rheumatology 68, no. 6 (May 26, 2016): 1483–92. http://dx.doi.org/10.1002/art.39572.

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Rocha-Viggiano, Ana K., Saray Aranda-Romo, Mariana Salgado-Bustamante, and Cesaré Ovando-Vázquez. "Meconium Microbiota Composition and Association with Birth Delivery Mode." Advanced Gut & Microbiome Research 2022 (November 7, 2022): 1–18. http://dx.doi.org/10.1155/2022/6077912.

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Recently, the intrauterine sterile environment theory has been questioned. Growing evidence shows that microbial in utero pioneer gut colonization could occur prebirth, and this initial colonization may play an important role in the development of the neonate immune system and setting up a niche for the adult-like microbiota. In this study, we compared the microbiota networks from public available meconium datasets from different countries. The findings showed differences at the genera level and were country-dependent. We generated and analyzed bacterial networks, at the genera level of meconium samples from c-section and vaginally delivery modes. Interestingly, bacterial networks from the c-section-delivered meconium samples tended to have a bigger diameter but fewer correlations, whereas the vaginally delivered meconium networks were smaller and with a higher number of correlations. Even more, the networks were similar in the delivery mode, even between countries, at the genera level. The c-section networks suggest incomplete colonization or important lack of bacteria, promoting the susceptibility of the network to receive new members, beneficial or pathogens. These results suggest that the network analysis contributes to the knowledge of microbiota composition, identifying microbial associations, despite the differences between the environment and country habits, and obtaining a better understanding of microbial gut colonization.

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Hussain, Shehnaz K., Tien S. Dong, Vatche Agopian, Joseph R. Pisegna, Francisco A. Durazo, Pedram Enayati, Vinay Sundaram, et al. "Dietary Protein, Fiber and Coffee Are Associated with Small Intestine Microbiome Composition and Diversity in Patients with Liver Cirrhosis." Nutrients 12, no. 5 (May 13, 2020): 1395. http://dx.doi.org/10.3390/nu12051395.

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The gut microbiome is a key factor in chronic liver disease progression. In prior research, we found that the duodenal microbiome was associated with sex, ethnicity, and cirrhosis complications. Here, we examined the association between diet and the duodenal microbiome in patients with liver cirrhosis. This study included 51 participants who completed a detailed food frequency questionnaire and donated duodenal biopsies for microbiome characterization by 16S ribosomal RNA gene sequencing. Data were analyzed for alpha diversity, beta diversity, and association of taxa abundance with diet quality and components using QIIME 2 pipelines. Diet quality was assessed through calculation of the Healthy Eating Index 2010. Participants with higher adherence to protein recommendations exhibited increased microbial richness and evenness (p = 0.03) and a different microbial profile compared to those with lower adherence (p = 0.03). Prevotella-9 and Agathobacter were increased in association with increased protein adherence. Fiber consumption was also associated with the duodenal microbial profile (p = 0.01), with several taxa exhibiting significantly decreased or increased abundance in association with fiber intake. Coffee drinking was associated with microbial richness and evenness (p = 0.001), and there was a dose–response association between coffee drinking and relative abundance of Veillonella (p = 0.01). We conclude that protein, fiber, and coffee are associated with diversity and composition of the duodenal microbiome in liver cirrhosis.

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Wang, Dong D., Qibin Qi, Zheng Wang, Mykhaylo Usyk, Daniela Sotres-Alvarez, Josiemer Mattei, Martha Tamez, et al. "The Gut Microbiome Modifies the Association Between a Mediterranean Diet and Diabetes in USA Hispanic/ Latino Population." Journal of Clinical Endocrinology & Metabolism 107, no. 3 (November 8, 2021): e924-e934. http://dx.doi.org/10.1210/clinem/dgab815.

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Abstract Context The interrelationships among the gut microbiome, the Mediterranean diet (MedDiet), and a clinical endpoint of diabetes is unknown. Objective To identify gut microbial features of a MedDiet and examine whether the association between MedDiet and diabetes varies across individuals with different gut microbial profiles. Methods This study included 543 diabetic, 805 prediabetic, and 394 normoglycemic participants from a cohort study of USA Hispanic/Latino men and women. Fecal samples were profiled using 16S rRNA gene sequencing. Adherence to MedDiet was evaluated by an index based on 2 24-hour dietary recalls. Results A greater MedDiet adherence was associated with higher abundances of major dietary fiber metabolizers (e.g., Faecalibacterium prausnitzii, false-discovery-rate–adjusted P [q] = 0.01), and lower abundances of biochemical specialists (e.g., Parabacteroides, q = 0.04). The gut microbiomes of participants with greater MedDiet adherence were enriched for functions involved in dietary fiber degradation but depleted for those related to sulfur reduction and lactose and galactose degradation. The associations between MedDiet adherence and diabetes prevalence were significantly stronger among participants with depleted abundance of Prevotella (pinteraction = 0.03 for diabetes, 0.02 for prediabetes/diabetes, and 0.02 for prediabetes). A 1-SD deviation increment in the MedDiet index was associated with 24% (odds ratio [OR] 0.76; 95% CI, 0.59-0.98) and 7% (OR 0.93; 95% CI, 0.72-1.20) lower odds of diabetes in Prevotella noncarriers and carriers, respectively. Conclusion Adherence to MedDiet is associated with diverse gut microorganisms and microbial functions. The inverse association between the MedDiet and diabetes prevalence varies significantly depending on gut microbial composition.

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Journal articles on the topic 'Microbial association'

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