Robust expansion of phylogeny for fast-growing genome sequence data

Massive sequencing of SARS-CoV-2 genomes has led to a great demand for adding new samples to a reference phylogeny instead of building the tree from scratch. To address such challenge, we proposed an algorithm 'TIPars' by integrating parsimony analysis with pre-computed ancestral sequences. Compared to four state-of-the-art methods on four benchmark datasets (SARS-CoV-2, Influenza virus, Newcastle disease virus and 16S rRNA genes), TIPars achieved the best performance in most tests. It took only 21 seconds to insert 100 SARS-CoV-2 genomes to a 100k-taxa reference tree using near 1.4 gigabytes of memory. Its efficient and accurate phylogenetic placements and incrementation for phylogenies with highly similar and divergent sequences suggest that it will be useful in a wide range of studies including pathogen molecular epidemiology, microbiome diversity and systematics.

The Relationship between Gut Microbiome and Cognition in Older Australians

Ageing is associated with changes in biological processes, including reductions in cognitive functions and gut microbiome diversity. However, not much is known about the relationship between cognition and the microbiome with increasing age. Therefore, we examined the relationship between the gut microbiome and cognition in 69 healthy participants aged 60–75 years. The gut microbiome was analysed with the 16S rRNA sequencing method. The cognitive assessment included the Cognitive Drug Research computerised assessment battery, which produced five cognitive factors corresponding to ‘Quality of Episodic Secondary Memory’, ‘Quality of Working Memory’, ‘Continuity of Attention, ‘Speed of Memory’ and ‘Power of Concentration’. Multiple linear regression showed that the bacterial family Carnobacteriaceae explained 9% of the variance in predicting Quality of Episodic Secondary Memory. Alcaligenaceae and Clostridiaceae explained 15% of the variance in predicting Quality of Working Memory; Bacteroidaceae, Barnesiellaceae, Rikenellaceae and Gemellaceae explained 11% of the variance in Power of Concentration. The present study provides specific evidence of a relationship between specific families of bacteria and different domains of cognition.

Milking it for all it's worth: The effects of environmental enrichment on maternal nurturance, lactation quality, and offspring social behavior

While alterations in the neonatal environment can have dramatic effects on offspring outcomes, the mechanisms that drive this phenomenon remain unclear. Breastfeeding confers robust benefits to offspring development, including those related to growth, immunity, and neurophysiology. Similarly, improving environmental complexity (i.e., environmental enrichment; EE) contributes developmental advantages to both humans and laboratory animal models. However, the impact of environmental context on maternal care and milk quality has not been thoroughly evaluated, nor are the biological underpinnings of EE on offspring development understood. Here, Sprague-Dawley rats were housed and bred in either EE or standard-housed (SD) conditions. Although EE dams gave birth to a larger number of pups, litters were standardized and cross-fostered across groups on postnatal day (P)1. Maternal milk samples were then collected on P1 (transitional milk phase) and P10 (mature milk phase) for analysis. While EE dams spent less time nursing, postnatal enrichment exposure was associated with heavier offspring bodyweights. Moreover, milk from EE dams had increased triglyceride levels compared to SD dams. Milk from EE mothers also contained a greater microbiome diversity and a significantly higher abundance of bacterial families related to bodyweight and energy metabolism. In addition to changes in lactational quality, we observed sex- and time-dependent effects of EE on offspring social behavior. Specifically, prenatal EE exposure was associated with greater sociability in females, while postnatal EE was associated with greater sociability in male offspring. Together, these results underscore the multidimensional impact of the combined neonatal and maternal environments on offspring development. These data also identify potential deficiencies in the quality of the "gold standard" laboratory housing condition and its impact on the welfare and design of translationally relevant animal models in biomedical research.

Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level

The influence of the microbiome on its host is well-documented, but the interplay of its members is not yet well-understood. Even for simple microbiomes, the interaction among members of the microbiome is difficult to study. Longitudinal studies provide a promising approach to studying such interactions through the temporal covariation of different taxonomic units. By contrast to most longitudinal studies, which span only a single host generation, we here present a post hoc analysis of a whole-genome dataset of 81 samples that follows microbiome composition for up to 180 host generations, which cover nearly 10 years. The microbiome diversity remained rather stable in replicated Drosophila melanogaster populations exposed to two different temperature regimes. The composition changed, however, systematically across replicates of the two temperature regimes. Significant associations between families, mostly specific to one temperature regime, indicate functional interdependence of different microbiome components. These associations also involve moderately abundant families, which emphasizes their functional importance, and highlights the importance of looking beyond the common constituents of the Drosophila microbiome.

Gardnerella Vaginalis in Recurrent Urinary Tract Infection is Associated with Dysbiosis of the Bladder Microbiome

Background: Recent studies on the urine microbiome have highlighted the importance of the gut-vagina-bladder axis in recurrent cystitis (RC). In particular, the role of Gardnerella as a covert pathogen that activates E. coli in animal experiments has been reported. Herein, we conducted a human bladder microbiome study to investigate the effect of Gardnerella on RC. Methods: Urine 16S ribosomal RNA gene sequencing via transurethral catheterization was conducted in the normal control group (NC) (n=18) and RC group (n=78). Results: The positive detection rate of Gardnerella species did not differ between the NC and RC groups (22.2% vs. 18.0%, p = 0.677). In addition, the Gardnerella-positive NC and Gardnerella-positive RC groups showed similar levels of microbiome diversity. The Gardnerella-positive group was categorized into three subgroups: Escherichia-dominant group, Gardnerella-dominant group, and Lactobacillus-dominant group, respectively. All of the Escherichia-dominant groups were associated with RC. Gardnerella-dominant or Lactobacillus-dominant groups expressed RC with symptoms when risk factors such as degree of Gardnerella proliferation or causative agents of bacterial vaginosis were present.Conclusion: Gardnerella can act as a covert pathogen of RC depending on other risk factors, and Gardnerella infection should be considered in patients with RC. New guideline recommendations regarding antibiotics selection based on a novel method to detect the cause of RC may be required to reduce antibiotics resistance.

Feed and Host Genetics Drive Microbiome Diversity with Resultant Consequences for Production Traits in Mass-Reared Black Soldier Fly (Hermetia illucens) Larvae

Mass rearing the black soldier fly, Hermetia illucens, for waste bioremediation and valorisation is gaining traction on a global scale. While the health and productivity of this species are underpinned by associations with microbial taxa, little is known about the factors that govern gut microbiome assembly, function, and contributions towards host phenotypic development in actively feeding larvae. In the present study, a 16S rDNA gene sequencing approach applied to a study system incorporating both feed substrate and genetic variation is used to address this knowledge gap. It is determined that the alpha diversity of larval gut bacterial communities is driven primarily by features of the larval feed substrate, including the diversity of exogenous bacterial populations. Microbiome beta diversity, however, demonstrated patterns of differentiation consistent with an influence of diet, larval genetic background, and a potential interaction between these factors. Moreover, evidence for an association between microbiome structure and the rate of larval fat accumulation was uncovered. Taxonomic enrichment analysis and clustering of putative functional gut profiles further suggested that feed-dependent turnover in microbiome communities is most likely to impact larval characteristics. Taken together, these findings indicate that host–microbiome interactions in this species are complex yet relevant to larval trait emergence.