In metagenomics, biological specimens are sometimes collected from host tissue that contains a high ratio of host to bacterial DNA. When shotgun metagenomics sequencing data are generated for these specimens, they normally contain a large fraction of host reads compared to microbial reads. Analyzing microbiome data with a high host ratio of reads can lead...
A complete analysis of the microbiome should combine taxonomic profiling with functional characterization to discover the full potential of an entire community of microorganisms. However, research teams often require specialized training and extensive computational infrastructure to establish an in-house suite of tools for processing shotgun metagenomic data – and even with the right know-how, the...
The skin is the body’s first line of defense, protecting the host against environmental or microbial insults by the imposition of a physical barrier. Upon microbial entry into wounds, innate immune cells generate antimicrobial proteins to prevent bacterial infections. A well-studied example is the innate immune circuits of IL-17 and IL-22, which are activated by...
Over the last decade, the field of metagenomics has grown extensively, leading to an exponential increase in sequencing data in public data repositories. Availability of this huge collection of data has accelerated the discovery of novel microbiome-related biomarkers and microbiome-based novel biomedical therapeutics. One of the key steps in identifying potential biomarkers or lead candidates...
Introduction The advent of metagenomic sequencing has led to significant advancements in our understanding of the microbiome in a wide variety of contexts, from the human body1 to farm animals2,3, soil, and marine environments4. Each unique environment provides its own set of challenges in accurate microbial identification, including low microbial biomass in ocean samples, PCR...
The human gut microbiome is a key modulator of human health. It is known to play important roles in the outcome of treatments and diseases, including acute lymphoblastic leukemia (ALL). Although survival rates of ALL exceed 90%, infectious complications still remain a challenge to disease prognosis and quality of life. Recent studies suggest a link...
By Barış Özdinç Dogs have been man’s best friend for centuries and continue to be popular pets today. According to the American Pet Products Association National Pet Owners Survey, 53.4% of American households own a dog. People love their dogs like family members and may be naturally interested in ways in which to improve...
Mobile phones have become essential to modern-day living; they are the main communication device for two-thirds of the human population (Kemp 2020). People handle their mobile phones up to 2000 times per day, which can total up to 3h and 37 minutes (Winnick 2016). Consequently, mobile phones have emerged as a fomite that could play...
There are so many different dog foods out there, with so many different health claims, that it can be confusing to choose the right one for your pet. Is a dry food better? Or a canned wet food? Do canned wet foods cause poor oral health? To answer these questions, Oba et al. (2022) sought...
Written by Baris Ozdinc The human gut microbiome is intimately linked to human health. Genetics, lifestyle and environmental factors all shape the human gut microbiome. Disease also significantly alters the gut microbiome, but how is not known for all illnesses. The gut microbiome in Human Immunodeficiency Virus (HIV) infection has been examined in the past...
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