... alpha diversity could predict depressive-like behaviors ... Pseudomonas spp. were positively associated with positive behaviors ... contributed to lipid metabolism pathways ...

... diagnostic and prognostic use of circulating microbiome DNA (cmDNA) signatures in lung cancer patients ... the early detection and recurrence models exhibited high degrees of accuracy and sensitivity ...

... strain-resolved microbial abundances improve machine learning predictions of ICB response and 12-month progression-free survival ... development of gut microbiome diagnostics or therapeutics should be tailored according to ICB treatment regimen ...

... a flexible DA method that can account for microbiome data characteristics and diverse experimental designs. ... extracts more informative biological signals while accounting for study-specific experimental conditions ...

... We introduce Greengenes2, a reference tree that unified genomic and 16S rRNA databases in a consistent, integrated resource. ... data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size ...

…the “Lunar Palace 365” mission, a 1-year-long isolation study… …On the basis of metagenomic, metaproteomic, and metabolomic analyses, the four potential psychobiotics improved mood mainly through three pathways related to nervous system functions…

…uses in-situ spatial technologies to characterize intratumoral bacteria the tumour microenvironment… …upregulation of inflammatory and cancer progression genes… …promote the detachment and invasion of single infected cancer cells…

...to test a range of different tools commonly used for metagenomic assembly, genome binning, taxonomic binning and taxonomic profiling...this work is really useful for the microbiome community, but we felt that there were several aspects of the writeup that could be improved upon...

... used correlation-adjusted regression to determine the percentage of variance in each pangenome feature … overall the species’ environments explained a larger proportion of variance ...

...examine potential confounders in COVID-19 microbiome studies by analysing two datasets... the amount of time spent in the ICU and the type of oxygen support explained most of the variation in the upper respiratory tract microbiome...

... difficult to visualize the overlap in strain genome contents when the number of genomes becomes large. PPanGGOLiN is a tool that addresses this problem...

...both diets were effective at restricting energy intake and improving some metabolic outcomes, with the probiotic group showing additional metabolic benefits along with shifts in specific bacteria

...by replacing the fungal database of HMS with 18 species of amphibians and reptiles (i.e. organisms not expected to be present in the human gut microbiome) and applying this to the human gut metagenome samples used in the previous paper, they are able to identify these species...

...typical sample sizes used in microbiome studies might simply be too low to ensure robust results. Rothschild et al. investigated this question by performing shotgun metagenomics sequencing of the stool of ~34,000 individuals...

...completed a comprehensive 16S rRNA gene survey of the microbiome of various tumor types (breast, lung, ovary, pancreas, melanoma, bone and brain).

...addressed the problem of high dimensionality in metagenomics data by clustering genes using the Approximate Nearest Neighbour algorithm to form co-abundant gene groups, or CAGs

...screened for microbial DNA and RNA in thousands of samples from The Cancer Genome Atlas… and demonstrated that the microbial sequences could be used to distinguish between cancer types

...patients who remained in remission following EEN for up to 24 weeks were dominated by secondary bile acids, whereas other patients were mainly dominated by primary bile acids

...this paper is an argument for the utility of rarefying data ... and a response to the “Waste Not, Want Not” paper

There is a lot of physiological heterogeneity even in healthy individuals. The ancient Ayurveda system of Indian medicine has a protocol for classifying individuals into 3 major prakritis or physiological phenotype groups.

... Kim et al. show that the administration of a bacterial community consisting of ... can lead to the depletion of VRE

...how are complex traits, those dependent on a large number of genes, transferred by HGT?

...the difference in the frequency of a compositional feature can best be analyzed relative to the frequency of another individual or set of features

... longitudinal human gut microbiome datasets of healthy adult to identify resident and transient members of microbiome.

Cystic Fibrosis (CF) may be most known for its effects on respiration, but less recognized is that people with CF have an earlier onset of colorectal cancer (CRC) than those without CF - up to 30 years earlier compared to the relative population. Dayama et al. find a link between the microbiome and human host that may explain some mechanisms why.

Many microbes in the human microbiome remain unknown. This issue is especially pervasive for individuals on non-Western diets since they are underrepresented in microbiome studies.

Typically microbiome studies can only claim to detect associations … in this case the authors use Mendelian Randomization, which theoretically can determine whether a given association is causal.

Tanoue et al., demonstrate a methodological pipeline for identifying a subset of the gut microbiome for immune modulation to help fight off cancer and infections

We enjoyed reading this paper as it showed a clear clinical use of next generation sequencing in the context of infectious diseases.

Variation at the bacterial strain level sheds light on functional differences amongst infant gut microbiomes from Eastern Europe.

...Armour et al. analyzed over 2000 metagenomics samples from 8 studies, which represented a range of diseases… since this is a pre-print hopefully the feedback below is helpful!

Altered viral populations have been observed in adults with IBD, but there has yet to be controlled experiments of phage dynamics in experimental mice models of IBD. In this study, Duerkop et al. find differences in bacteriophage after induction of colitis in mice.

...identified 34 gut-microbiota associated epitopes and demonstrated that these were abnormal in the gut of ASD children in terms of composition and was in turn associated with abnormal IgA levels.

Do bacterial species exist other than as a functional delineation? Exclusivity says no.

The researchers harness the potential of this deeply phenotyped population by focussing on common diseases and prescription medications used. Several novel associations were described, in addition to replicated associations from previous work across IBD and T2DM.

In this report Hakim, et al., show that the composition of the gut microbiome could be used to predict if pediatric acute lymphoblastic leukemia (ALL) patients will have an infection throughout chemotherapy.

... fecal metabolome can be used as an intermediate phenotype to study host-microbiome interactions.

...a new method of aggregating the results of multiple metagenome assembly programs together to produce a better set of assemblies.

Stemming from the Earth Microbiome Project, McDonald et al. employ citizen-scientists to provide microbiome samples for deeper comparison of human gut vs environmental microbiome diversity, human stool metabolomics and the influence of overgrowth during room temperature shipping on correlation analysis.

Maier et al., analyzed the growth of 40 representative isolates of the gut microbiome under a high-throughput growth inhibition screen with 1,197 compounds, finding that 24% of human-targeted drugs had inhibitory effects on gut commensals.

... high-fiber rich diet promotes specific gut bacteria capable of producing SCFA which in turn improves glucose homeostasis in Type 2 diabetic patients.

...the replicons confer a substantial amount of redundancy in essential genes found in the genome. They also highlight insights that would not have been possible without also performing in silico metabolic reconstruction.

Johns et al., use a high throughput GFP reporting screen to test the regulatory features of over 29,000 unidirectional intergenic regions from 184 different prokaryotic genomes.

This group examined the contribution of host genetics to microbiome composition and concluded that the gut microbiome overall is not heritable, but instead is predominantly shaped by environmental factors.

...designed to classify features into contaminant or non-contaminant categories based on one or two deterministic patterns observed in empirical data

Parks et al. look to fix problems with existing taxonomy. They propose a novel standardized bacterial taxonomy based on a concatenated protein phylogeny.

...different patterns of functional prevalence would be found if the RNA and DNA were analyzed separately.

...an optimized method to sequence full-length small subunit ribosomal RNA by combining novel sequencing and molecular tagging protocols.

In this paper, Duvallet et al. present an effective way to conduct meta-analyses of 16S-based case-control studies of human-gut associated diseases. By reprocessing the datasets with a common bioinformatic pipeline and collapsing to the genus level, significant associations can be compared across studies for the same disease and across multiple studies of different diseases.

...relative abundance data cannot be used to determine directional changes in taxa abundance or the biological relevance of these shifts. Vandeputte et al., attempt to solve this issue by measuring absolute bacterial loads of samples in combination with relative abundance information from 16S profiling to create quantitative microbiome profiles.

...combining the oral microbiome and stool microbiome datasets distinguished those with cancer and those with colonic polyps compared to controls with a relatively high specificity. They also found that some of these oral microbes are enriched in pediatric Crohn’s disease biopsies...

...evidence that MIA-mediated abnormal behavioural phenotypes requires both the presence of segmented filamentous bacteria (SBF) and viral immune activation during pregnancy in mice. These two factors induce the differentiation of IL-17-producing T helper 17 (TH17) cells in pregnant mothers. Their offspring display behavioural abnormalities, which are associated with the presence of cortical patches in the somatosensory cortex of the brain.

This paper is a great example of data-mining available shotgun metagenomics sequencing (MGS) datasets for novel inference. They focus on Blastocystis, a genus of unicellular eukaryotic microorganisms in the Stramenopile phylum. Morphologically strains are similar, but genetically can be extremely different.