Topological Data Analysis Highlights Novel Geographical Signatures of the Human Gut Microbiome

Informatics for your Gut: at the Interface of Nutrition, the Microbiome, and Technology

BACKGROUND

A significant portion of individuals in the United States and worldwide experience diseases related to or driven by diet. As research surrounding user-centered design and the microbiome grows, movement of the spectrum of translational science from bench to bedside for improvement of human health through nutrition becomes more accessible. In this literature survey, we examined recent literature examining informatics research at the interface of nutrition and the microbiome.

OBJECTIVES

The objective of this survey was to synthesize recent literature describing how technology is being applied to understand health at the interface of nutrition and the microbiome focusing on the perspective of the consumer.

METHODS

A survey of the literature published between January 1, 2021 and October 10, 2022 was performed using the PubMed database and resulting literature was evaluated against inclusion and exclusion criteria.

RESULTS

A total of 139 papers were retrieved and evaluated against inclusion and exclusion criteria. After evaluation, 45 papers were reviewed in depth revealing four major themes: (1) microbiome and diet, (2) usability,(3) reproducibility and rigor, and (4) precision medicine and precision nutrition.

CONCLUSIONS

A review of the relationships between current literature on technology, nutrition and the microbiome, and self-management of dietary patterns was performed. Major themes that emerged from this survey revealed exciting new horizons for consumer management of diet and disease, as well as progress towards elucidating the relationship between diet, the microbiome, and health outcomes. The survey revealed continuing interest in the study of diet-related disease and the microbiome and acknowledgement of needs for data re-use, sharing, and unbiased and rigorous measurement of the microbiome. The literature also showed trends toward enhancing the usability of digital interventions to support consumer health and home management, and consensus building around how precision medicine and precision nutrition may be applied in the future to improve human health outcomes and prevent diet-related disease.

Alteration of Gut Microbial Metabolites in the Systemic Circulation of Patients with Parkinson's Disease

BACKGROUND

Emerging evidence suggests that gut dysbiosis contributes to Parkinson's disease (PD) by signaling through microbial metabolites. Hippuric acid (HA), indole derivatives, and secondary bile acids are among the most common gut metabolites.

OBJECTIVE

To examine the relationship of systemic concentrations of these microbial metabolites associated with changes of gut microbiota, PD status, and severity of PD.

METHODS

We enrolled 56 patients with PD and 43 age- and sex-matched healthy participants. Motor and cognitive severity were assessed with Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) part III motor score and the Mini-Mental State Examination (MMSE), respectively. Plasma concentrations of targeted gut metabolites were measured with liquid chromatography-tandem mass spectrometry. Gut microbiota was analyzed with shotgun metagenomic sequencing.

RESULTS

Compared with controls, PD patients had significantly higher plasma levels of HA, indole-3-propionic acid (IPA), deoxycholic acid (DCA), and glycodeoxycholic acid (GDCA). After adjustment for age and sex in a multivariate logistic regression analysis, plasma levels of HA (odds ratio [OR] 3.21, p < 0.001), IPA (OR 2.59, p = 0.031), and GDCA (OR 2.82, p = 0.036) were associated with positive PD status. Concentrations of these gut metabolites did not correlate with MDS-UPDRS part III score or MMSE after adjustment for confounders. Microbial metabolite levels were associated with the relative abundance of pro-inflammatory gut bacteria.

CONCLUSION

Aberrant gut microbial metabolites of HA, indole derivatives and secondary bile acids associated with specific gut microbiota changes were observed in patients with PD.

Gastrointestinal Manifestations of Coronavirus Disease 2019 Across the United States: A Multicenter Cohort Study

Background and Aims

Gastrointestinal (GI) symptoms occur among patients diagnosed with coronavirus disease 2019 (COVID-19), and there is clear evidence that SARS-CoV-2, the causative pathogen, infects the GI tract. In this large, multicenter cohort study, we evaluated variations in gastrointestinal and hepatic manifestations of COVID-19 throughout the United States (US).

Methods

Patients hospitalized with a positive COVID-19 test prior to October 2020 were identified at 7 US academic centers. Demographics, presenting symptoms, laboratory data, and hospitalization outcomes were abstracted. Descriptive and regression analyses were used to evaluate GI manifestations and their potential predictors.

Results

Among 2031 hospitalized patients with COVID-19, GI symptoms were present in 18.9%; diarrhea was the most common (15.2%), followed by nausea and/or vomiting (12.6%) and abdominal pain (6.0%). GI symptoms were less common in the Western cohort (16.0%) than the Northeastern (25.6%) and Midwestern (26.7%) cohorts. Compared to nonintensive care unit (ICU) patients, ICU patients had a higher prevalence of abnormal aspartate aminotransferase (58.1% vs 37.3%; P < .01), alanine aminotransferase (37.5% vs 29.3%; P = .01), and total bilirubin (12.7% vs 9.0%; P < .01). ICU patients also had a higher mortality rate (22.7% vs 4.7%; P < .01). Chronic liver disease was associated with the development of GI symptoms. Abnormal aspartate aminotransferase or alanine aminotransferase was associated with an increased risk of ICU admission.

Conclusion

We present the largest multicenter cohort of patients with COVID-19 across the United States. GI manifestations were common among patients hospitalized with COVID-19, although there was significant variability in prevalence and predictors across the United States.