Bioinformatic approaches for studying the microbiome of fermented food

LH Walsh, M Coakley, AM Walsh… - Critical Reviews in …, 2023 - Taylor & Francis
High-throughput DNA sequencing-based approaches continue to revolutionise our
understanding of microbial ecosystems, including those associated with fermented foods …

Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity

JP Shaffer, LF Nothias, LR Thompson, JG Sanders… - Nature …, 2022 - nature.com
Despite advances in sequencing, lack of standardization makes comparisons across studies
challenging and hampers insights into the structure and function of microbial communities …

Translocation of viable gut microbiota to mesenteric adipose drives formation of creeping fat in humans

CWY Ha, A Martin, GD Sepich-Poore, B Shi, Y Wang… - Cell, 2020 - cell.com
A mysterious feature of Crohn's disease (CD) is the extra-intestinal manifestation of"
creeping fat"(CrF), defined as expansion of mesenteric adipose tissue around the inflamed …

Applications and comparison of dimensionality reduction methods for microbiome data

G Armstrong, G Rahman, C Martino… - Frontiers in …, 2022 - frontiersin.org
Dimensionality reduction techniques are a key component of most microbiome studies,
providing both the ability to tractably visualize complex microbiome datasets and the starting …

Acetate reprograms gut microbiota during alcohol consumption

C Martino, LS Zaramela, B Gao, M Embree… - Nature …, 2022 - nature.com
Liver damage due to chronic alcohol use is among the most prevalent liver diseases.
Alcohol consumption frequency is a strong factor of microbiota variance. Here we use …

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis

RC Brewer, TV Lanz, CR Hale… - Science translational …, 2023 - science.org
Periodontal disease is more common in individuals with rheumatoid arthritis (RA) who have
detectable anti-citrullinated protein antibodies (ACPAs), implicating oral mucosal …

Microplastics as hubs enriching antibiotic-resistant bacteria and pathogens in municipal activated sludge

DN Pham, L Clark, M Li - Journal of Hazardous Materials Letters, 2021 - Elsevier
Microplastics can serve as carriers of antibiotic-resistant bacteria (ARB) and pathogens,
representing a pressing concern to aquatic biota and human health. Activated sludge units …

Terrestrial-type nitrogen-fixing symbiosis between seagrass and a marine bacterium

W Mohr, N Lehnen, S Ahmerkamp, HK Marchant… - Nature, 2021 - nature.com
Symbiotic N2-fixing microorganisms have a crucial role in the assimilation of nitrogen by
eukaryotes in nitrogen-limited environments,–. Particularly among land plants, N2-fixing …

Effects of 'healthy'fecal microbiota transplantation against the deterioration of depression in fawn-hooded rats

B Hu, P Das, X Lv, M Shi, J Aa, K Wang, L Duan… - Msystems, 2022 - Am Soc Microbiol
Depression is a recurrent, heterogeneous mood disorder occurring in more than 260 million
people worldwide. Gut microbiome dysbiosis is associated with the development of …

[HTML][HTML] Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing

F Fouladi, MJ Bailey, WB Patterson, M Sioda… - Environment …, 2020 - Elsevier
Animal work indicates exposure to air pollutants may alter the composition of the gut
microbiota. This study examined relationships between air pollutants and the gut …