Evaluating supervised and unsupervised background noise correction in human gut microbiome data

Quantifying bias introduced by sample collection in relative and absolute microbiome measurements

To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidence that measurement of the total count and concentration of microbes in the gut, or 'absolute abundance', provides a richer source of information than relative abundance and can correct some conclusions drawn from relative abundance data. However, little is known about how preservative choice can affect these measurements. In this study, we investigated how two common preservatives and short-term storage conditions impact relative and absolute microbial measurements. OMNIgene GUT OMR-200 yields lower metagenomic taxonomic variation between different storage temperatures, whereas Zymo DNA/RNA Shield yields lower metatranscriptomic taxonomic variation. Absolute abundance quantification reveals two different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. Based on these results, we recommend OMNIgene GUT OMR-200 preservative for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and we strongly encourage absolute quantification for microbial measurements.

Diversified Shifts in the Cross Talk between Members of the Gut Microbiota and Development of Coronary Artery Diseases

Coronary artery disease (CAD) is one of leading causes of mortality worldwide. Studies on roles that the gut microbiota plays in development of atherosclerosis or acute myocardial infarction (AMI) have been widely reported. However, the gut microbiota is affected by many factors, including age, body mass index (BMI), and hypertension, that lead to high CAD risk. However, the associations between gut microbiota and CAD development or other CAD risk factors remain unexplored. Here, we performed a 16S RNA gene sequencing analysis of 306 fecal samples collected from patients with mild coronary stenosis (MCS; n = 36), stable angina (SA; n = 91), unstable angina (UA; n = 48), and acute myocardial infarction (AMI; n = 66) and 65 non-CAD controls. Using a noise-corrected method based on principal-component analysis (PCA) and the random forest algorithm, we identified the interference with gut microbial profiling of multiple factors (including age, gender, BMI, and hypertension) that potentially contributed significantly to the development of CAD. After correction of noise interference from certain interfering factors, we found consistent indicator microbiota organisms (such as Vampirovibrio, Ruminococcus, and Eisenbergiella) associated with the presence of MCS, SA, and AMI. Establishment of a diagnostic model revealed better performance in early CAD than clinical indexes with indicator microbes. Furthermore, indicator microbes can improve the accuracy of clinical indexes for the diagnosis of AMI. Additionally, we found that the microbial indicators of AMI Sporobacter and Eisenbergiella showed consistent positive and negative correlations to the clinical indexes creatine kinase (CK) and hemoglobin (Hb), respectively. As a control indicator of AMI, Dorea was negatively correlated with CK but positively correlated with Hb. IMPORTANCE Our study discovered the effect of confounding factors on gut microbial variations and identified gut microbial indicators possibly associated with the CAD development after noise correction. Our discovered indicator microbes may have potential for diagnosis or therapy of cardiovascular disorders.

Multiomic analysis reveals microbiome-related relationships between cocaine use and metabolites

OBJECTIVE

Over 19 million individuals globally have a cocaine use disorder, a significant public health crisis. Cocaine has also been associated with a pro-inflammatory state and recently with imbalances in the intestinal microbiota as compared to nonuse. The objective of this pilot study was to characterize the gut microbiota and plasma metabolites in people with HIV (PWH) who use cocaine compared with those who do not.

DESIGN

Cross-sectional study.

METHODS

A pilot study in PWH was conducted on 25 cocaine users and 25 cocaine nonusers from the Miami Adult Studies on HIV cohort. Stool samples and blood plasma were collected. Bacterial composition was characterized using 16S rRNA sequencing. Metabolomics in plasma were determined using gas and liquid chromatography/mass spectrometry.

RESULTS

The relative abundances of the Lachnopspira genus, Oscillospira genus, Bifidobacterium adolescentis species, and Euryarchaeota phylum were significantly higher in the cocaine- using PWH compared to cocaine-nonusing PWH. Cocaine-use was associated with higher levels of several metabolites: products of dopamine catabolism (3-methoxytyrosine and 3-methoxytyramine sulfate), phenylacetate, benzoate, butyrate, and butyrylglycine.

CONCLUSIONS

Cocaine use was associated with higher abundances of taxa and metabolites known to be associated with pathogenic states that include gastrointestinal conditions. Understanding key intestinal bacterial functional pathways that are altered due to cocaine use in PWH will provide a better understanding of the relationships between the host intestinal microbiome and potentially provide novel treatments to improve health.

Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology

Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.