No abstract

Magnetospirillum sp. strain AMB-1 is a Gram-negative alpha-proteobacterium that synthesizes nano-sized magnetites, referred to as magnetosomes, aligned intracellularly in a chain. The potential of this nano-sized material is growing and will be applicable to broad research areas. It has been expected that genome analysis would elucidate the mechanism of magnetosome formation by magnetic bacteria. Here we describe the genome of Magnetospirillum sp. AMB-1 wild type, which consists of a single circular chromosome of 4967148 bp. For identification of genes required for magnetosome formation, transposon mutagenesis and determination of magnetosome membrane proteins were performed. Analysis of a non-magnetic transposon mutant library focused on three unknown genes from 2752 unknown genes and three genes from 205 signal transduction genes. Partial proteome analysis of the magnetosome membrane revealed that the membrane contains numerous oxidation/reduction proteins and a signal response regulator that may function in magnetotaxis. Thus, oxidation/reduction proteins and elaborate multidomain signaling proteins were analyzed. This comprehensive genome analysis will enable resolution of the mechanisms of magnetosome formation and provide a template to determine how magnetic bacteria maintain a species-specific, nano-sized, magnetic single domain and paramagnetic morphology.

Actin-targeting macrolides comprise a large, structurally diverse group of cytotoxins isolated from remarkably dissimilar micro- and macroorganisms. In spite of their disparate origins and structures, many of these compounds bind actin at the same site and exhibit structural relationships reminiscent of modular, combinatorial drug libraries. Here we investigate biosynthesis and evolution of three compound groups: misakinolides, scytophycin-type compounds and luminaolides. For misakinolides from the sponge Theonella swinhoei WA, our data suggest production by an uncultivated 'Entotheonella' symbiont, further supporting the relevance of these bacteria as sources of bioactive polyketides and peptides in sponges. Insights into misakinolide biosynthesis permitted targeted genome mining for other members, providing a cyanobacterial luminaolide producer as the first cultivated source for this dimeric compound family. The data indicate that this polyketide family is bacteria-derived and that the unusual macrolide diversity is the result of combinatorial pathway modularity for some compounds and of convergent evolution for others.

Single-cell genomics enabled the exploration of cellular diversity in a broad range of biological samples 1, 2 . Nowadays, the use of this technique allows us to identify the genomes of uncultivable microorganism 3, 4 , genetic mosaicism in tissues 5 , and intra-tumor heterogeneity 6 , which brings new perspectives to our understanding by revealing the role of individual cells in the biology of complex ecosystems and organisms. However, we still face several technical challenges in the sample preparation process, including effective isolation and lysis of single cells, uniform amplification of whole genome, quality assessment of single-cell amplified genomes (SAGs), sequencing library preparation, and sequencing analysis. Among all, to maximize the quality and throughput of single-cell sequencing, there is a great demand for novel techniques, which enable massively parallel whole genome amplification (WGA) with high accuracy.Microfluidic-based WGA represents one approach to achieve high-throughput and high fidelity single cell genomics. Microfluidic devices, including in-house 7-9 and commercially available valve-controlled microfluidic circuit (Fluidigm C1) 10, 11 and microwell 12, 13 , can integrate labor-intensive experimental WGA processes in a single, closed device and minimize the running cost and the risk of contamination that frequently occurs in bench-top experimentation. The reaction in microfluidic environment offers advantages over tube-based approaches, including improved reaction efficiency and detection sensitivity at the single-molecule level. In particular, droplet microfluidics has garnered the attention due to its scalability for various single cell studies 14 . Recently, we and other groups also developed the compartmented droplet multiple displacement amplification (cd-MDA) technique for bias-less single-cell WGA [15][16][17][18] . By distributing and amplifying single-cell genome

Regular exercise reduces the risks for cardiovascular diseases. Although the gut microbiota has been associated with fitness level and cardiometabolic risk factors, the effects of exercise‐induced gut microbiota changes in elderly individuals are unclear. This study evaluated whether endurance exercise modulates the gut microbiota in elderly subjects, and whether these changes are associated with host cardiometabolic phenotypes. In a randomized crossover trial, 33 elderly Japanese men participated in a 5‐week endurance exercise program. 16S rRNA gene‐based metagenomic analyses revealed that the effect of endurance exercise on gut microbiota diversity was not greater than interindividual differences, whereas changes in α‐diversity indices during intervention were negatively correlated with changes in systolic and diastolic blood pressure, especially during exercise. Microbial composition analyses showed that the relative abundance of Clostridium difficile significantly decreased, whereas that of Oscillospira significantly increased during exercise as compared to the control period. The changes in these taxa were correlated with the changes in several cardiometabolic risk factors. The findings indicate that short‐term endurance exercise has little effect on gut microbiota in elderly individuals, and that the changes in gut microbiota were associated with cardiometabolic risk factors, such as systolic and diastolic blood pressure, providing preliminary insight into the associations between the gut microbiota and cardiometabolic phenotypes.