Aspergillus oryzae is an industrially useful species, of which various strains have been identified; however, their genetic relationships remain unclear. A. oryzae was previously thought to be asexual and unable to undergo crossbreeding. However, recent studies revealed the sexual reproduction of Aspergillus flavus, a species closely related to A. oryzae. To investigate potential sexual reproduction in A. oryzae and evolutionary history among A. oryzae and A. flavus strains, we assembled 82 draft genomes of A. oryzae strains used practically. The phylogenetic tree of concatenated genes confirmed that A. oryzae was monophyletic and nested in one of the clades of A. flavus but formed several clades with different genomic structures. Our results suggest that A. oryzae strains have undergone multiple inter-genomic recombination events between A. oryzae ancestors, although sexual recombination among domesticated species did not appear to have occurred during the domestication process, at least in the past few decades. Through inter- and intra-cladal comparative analysis, we found that evolutionary pressure induced by the domestication of A. oryzae appears to selectively cause non-synonymous and gap mutations in genes involved in fermentation characteristics, as well as intra-genomic rearrangements, with the conservation of industrially useful catalytic enzyme-encoding genes.
Background: Bifidobacterium longum supplementation can be used to regulate bowel movement; however, individuals vary in the response to B. longum treatment. One putative factor is the gut microbiota; recent studies have reported that the gut microbiota mediates diet or drug effects. Here, we investigated intestinal features related to B. longum effectiveness in increasing bowel movement frequency.
Results: A randomized, double-blind controlled crossover trial was conducted with twenty Japanese subjects selected from 50 participants. The subjects received a two-week dietary intervention consisting of B. longum in acid-resistant seamless capsules or similarly encapsulated starch powder. Bowel movement frequency was recorded daily, and time-series fecal collection was conducted for metabologenomic analyses. There were differences among subjects in B. longum intake-induced bowel movement frequency. The responders were predictable by machine learning based on the metabologenomic features of the fecal samples collected before B. longum intake. Between responders and non-responders, the abundances of nine bacterial genera and of three compounds were significantly different.
Conclusions: Thus, the gut microbiome and metabolome composition have a strong impact on B. longum supplementation effectiveness in increasing bowel movement frequency, and gut metabologenomics enables B. longum supplementation effect prediction before intake. These findings have implications for the development of personalized probiotic treatments.
Trial registration: UMIN-CTR, UMIN000018924. Registered 07 September 2015, https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000021894
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