Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter?

Non-human-associated microbial communities play important biological roles, but they remain less understood than human-associated communities. Here, we assess the impact of key environmental sample properties on a variety of state-of-the-art metagenomic analysis methods. In simulated datasets, all methods performed similarly at high taxonomic ranks, but newer marker-based methods incorporating metagenomic assembled genomes outperformed others at lower taxonomic levels.

Oral microbial signatures associated with age and frailty in Canadian adults.

This study aimed to assess the association between the oral microbiome, age, and frailty. Data and saliva samples were obtained from male and female participants aged 35-70 years (n = 1357). Saliva samples were analysed by 16S rRNA gene sequencing and differences in microbial diversity and community compositions were examined in relation to chronological age and the frailty index (FI).

Investigating the oral microbiome in retrospective and prospective cases of prostate, colon, and breast cancer.

The human microbiome has been proposed as a potentially useful biomarker for several cancers. To examine this, we made use of salivary samples from the Atlantic Partnership for Tomorrow's Health (PATH) project and Alberta's Tomorrow Project (ATP). Sample selection was divided into both a retrospective and prospective case control design examining prostate, breast, and colon cancer.

Plant-Based Diets and Cancer Risk: What is the Evidence?

Purpose Of Review: The purpose of this review is to summarize the recent (past 5 years) available evidence regarding the association between plant-based diets on cancer risk from clinical trials and observational studies. Biological mechanisms and gaps in the current literature will also be discussed.

Recent Findings: There is a lack of intervention studies but there are abundant observational studies assessing the association between plant-based diets and cancer risk, including multiple longitudinal cohort studies and similar data from case-control studies that demonstrate a decreased overall cancer risk with plant-based diets.

Microbiome differential abundance methods produce different results across 38 datasets.

Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies systematically exploring the appropriateness of using these tools interchangeably, and the scale and significance of the differences between them.

Investigation of the impact of commonly used medications on the oral microbiome of individuals living without major chronic conditions.

Background: Commonly used medications produce changes in the gut microbiota, however, the impact of these medications on the composition of the oral microbiota is understudied.

Methods: Saliva samples were obtained from 846 females and 368 males aged 35-69 years from a Canadian population cohort, the Atlantic Partnership for Tomorrow's Health (PATH). Samples were analyzed by 16S rRNA gene sequencing and differences in microbial community compositions between nonusers, single-, and multi-drug users as well as the 3 most commonly used medications (thyroid hormones, statins, and proton pump inhibitors (PPI)) were examined.

Identifying biases and their potential solutions in human microbiome studies.

Advances in DNA sequencing technology have vastly improved the ability of researchers to explore the microbial inhabitants of the human body. Unfortunately, while these studies have uncovered the importance of these microbial communities to our health, they often do not result in similar findings. One possible reason for the disagreement in these results is due to the multitude of systemic biases that are introduced during sequence-based microbiome studies.

An in vivo genome-wide shRNA screen identifies BCL6 as a targetable biomarker of paclitaxel resistance in breast cancer.

Paclitaxel is a common breast cancer drug; however, some tumors are resistant. The identification of biomarkers for paclitaxel resistance or sensitivity would enable the development of strategies to improve treatment efficacy. A genome-wide in vivo shRNA screen was performed on paclitaxel-treated mice with MDA-MB-231 tumors to identify genes associated with paclitaxel sensitivity or resistance.

Harnessing the plant microbiome to promote the growth of agricultural crops.

The rhizosphere microbiome is composed of diverse microbial organisms, including archaea, viruses, fungi, bacteria as well as eukaryotic microorganisms, which occupy a narrow region of soil directly associated with plant roots. The interactions between these microorganisms and the plant can be commensal, beneficial or pathogenic. These microorganisms can also interact with each other, either competitively or synergistically.

Assessing the Variation within the Oral Microbiome of Healthy Adults.

More than 1,000 different species of microbes have been found to live within the human oral cavity, where they play important roles in maintaining both oral and systemic health. Several studies have identified the core members of this microbial community; however, the factors that determine oral microbiome composition are not well understood. In this study, we exam the salivary oral microbiome of 1,049 Atlantic Canadians using 16S rRNA gene sequencing to determine which dietary, lifestyle, and anthropometric features play a role in shaping microbial community composition.

Metagenomic Functional Shifts to Plant Induced Environmental Changes.

The (wild blueberry) agricultural system involves transformation of the environment surrounding the plant to intensify plant propagation and to improve fruit yield, and therefore is an advantageous model to study the interaction between soil microorganisms and plant-host interactions. We studied this system to address the question of a trade-off between microbial adaptation to a plant-influenced environment and its general metabolic capabilities. We found that many basic metabolic functions were similarly represented in bulk soil and rhizosphere microbiomes overall.

Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia.

Acute lymphoblastic leukemia is the most common pediatric cancer. Fortunately, survival rates exceed 90%, however, infectious complications remain a significant issue that can cause reductions in the quality of life and prognosis of patients. Recently, numerous studies have linked shifts in the gut microbiome composition to infection events in various hematological malignances including acute lymphoblastic leukemia (ALL).

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches.

High-depth sequencing of universal marker genes such as the 16S rRNA gene is a common strategy to profile microbial communities. Traditionally, sequence reads are clustered into operational taxonomic units (OTUs) at a defined identity threshold to avoid sequencing errors generating spurious taxonomic units. However, there have been numerous bioinformatic packages recently released that attempt to correct sequencing errors to determine real biological sequences at single nucleotide resolution by generating amplicon sequence variants (ASVs).