Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation.

Sample preservation often impedes efforts to generate high-quality reference genomes or pangenomes for Earth's more than 2 million plant and animal species due to nucleotide degradation. Here we compare the impacts of storage methods including solution type, temperature, and time on DNA quality and Oxford Nanopore long-read sequencing quality in 9 fish and 4 plant species. We show 95% ethanol largely protects against degradation for fish blood (22 °C, ≤6 weeks) and plant tissue (4 °C, ≤3 weeks). From this furthest storage timepoint, we assemble high-quality reference genomes of 3 fish and 2 plant species with contiguity (contig N50) and completeness (BUSCO) that achieve the Vertebrate Genome Project benchmarking standards. For epigenetic applications, we also report methylation frequency compared to liquid nitrogen control. The results presented here remove the necessity for cryogenic storage in many long read applications and provide a framework for future studies focused on sampling in remote locations, which may represent a large portion of the future sequencing of novel organisms.

The Microbiota-Gut-Brain Axis in Alzheimer's Disease: A Review of Taxonomic Alterations and Potential Avenues for Interventions.

OBJECTIVE: The gut microbiome is a complex community of microorganisms that inhabit the gastrointestinal tract. The microbiota-gut-brain axis encompasses a bidirectional communication system that allows the gut to influence the brain via neural, endocrine, immune, and metabolic signaling. Differences in the gut microbiome have been associated with psychiatric and neurological disorders, including Alzheimer's Disease (ad). Understanding these ad-associated alterations may offer novel insight into the pathology and treatment of ad. METHOD: We conducted a narrative review of clinical studies investigating the gut microbiome in ad, organizing the results by phyla to understand the biological contributions of the gut microbial community to ad pathology and clinical features. We also reviewed randomized clinical trials of interventions targeting the microbiome to ameliorate ad symptoms and biomarkers. RESULTS: Alpha diversity is reduced in patients with ad. Within Firmicutes, taxa that produce beneficial metabolites are reduced in ad, including Clostridiaceae, Lachnospiraceae, Ruminococcus, and Eubacterium. Within Bacteroidetes, findings were mixed, with studies showing either reduced or increased abundance of Bacteroides in mild cognitive impairment or ad patients. Proteobacteria that produce toxins tend to be increased in ad patients, including Escherichia/Shigella. A Mediterranean-ketogenic dietary intervention significantly increased beneficial short-chain fatty acids and taxa that were inversely correlated with changes in ad pathological markers. Probiotic supplementation with Lactobacillus spp. and Bifidobacterium spp. improved cognitive function and reduced inflammatory and metabolic markers in patients with ad. CONCLUSIONS: The gut microbiome may provide insight into ad pathology and be a novel target for intervention. Potential therapeutics include probiotics and dietary intervention.

Neurobiology of loneliness: a systematic review.

Loneliness is associated with increased morbidity and mortality. Deeper understanding of neurobiological mechanisms underlying loneliness is needed to identify potential intervention targets. We did not find any systematic review of neurobiology of loneliness. Using MEDLINE and PsycINFO online databases, we conducted a search for peer-reviewed publications examining loneliness and neurobiology. We identified 41 studies (n = 16,771 participants) that had employed various methods including computer tomography (CT), structural magnetic resonance imaging (MRI), functional MRI (fMRI), electroencephalography (EEG), diffusion tensor imaging (DTI), single-photon emission computed tomography (SPECT), positron emission tomography (PET), and post-mortem brain tissue RNA analysis or pathological analysis. Our synthesis of the published findings shows abnormal structure (gray matter volume or white matter integrity) and/or activity (response to pleasant versus stressful images in social versus nonsocial contexts) in the prefrontal cortex (especially medial and dorsolateral), insula (particularly anterior), amygdala, hippocampus, and posterior superior temporal cortex. The findings related to ventral striatum and cerebellum were mixed. fMRI studies reported links between loneliness and differential activation of attentional networks, visual networks, and default mode network. Loneliness was also related to biological markers associated with Alzheimer's disease (e.g., amyloid and tau burden). Although the published investigations have limitations, this review suggests relationships of loneliness with altered structure and function in specific brain regions and networks. We found a notable overlap in the regions involved in loneliness and compassion, the two personality traits that are inversely correlated in previous studies. We have offered recommendations for future research studies of neurobiology of loneliness.

The Gut Microbiome, Aging, and Longevity: A Systematic Review.

Aging is determined by complex interactions among genetic and environmental factors. Increasing evidence suggests that the gut microbiome lies at the core of many age-associated changes, including immune system dysregulation and susceptibility to diseases. The gut microbiota undergoes extensive changes across the lifespan, and age-related processes may influence the gut microbiota and its related metabolic alterations. The aim of this systematic review was to summarize the current literature on aging-associated alterations in diversity, composition, and functional features of the gut microbiota. We identified 27 empirical human studies of normal and successful aging suitable for inclusion. Alpha diversity of microbial taxa, functional pathways, and metabolites was higher in older adults, particularly among the oldest-old adults, compared to younger individuals. Beta diversity distances significantly differed across various developmental stages and were different even between oldest-old and younger-old adults. Differences in taxonomic composition and functional potential varied across studies, but Akkermansia was most consistently reported to be relatively more abundant with aging, whereas Faecalibacterium, Bacteroidaceae, and Lachnospiraceae were relatively reduced. Older adults have reduced pathways related to carbohydrate metabolism and amino acid synthesis; however, oldest-old adults exhibited functional differences that distinguished their microbiota from that of young-old adults, such as greater potential for short-chain fatty acid production and increased butyrate derivatives. Although a definitive interpretation is limited by the cross-sectional design of published reports, we integrated findings of microbial composition and downstream functional pathways and metabolites, offering possible explanations regarding age-related processes.