Laboratory-adapted and wild-type black soldier flies express differential plasticity in bioconversion and nutrition when reared on urban food waste streams.

BACKGROUND: The black soldier fly (BSF) offers a potential solution to address shortages of feed and food sources; however, selecting effective rearing substrates remains a major hurdle in BSF farming. In an urban area like Singapore, current practice is based on rearing BSF on homogeneous waste streams (e.g., spent brewery grains or okara) because heterogeneous food wastes (e.g., mixed kitchen/canteen waste or surplus cooked food) present several operational challenges with respect to the standardization of development, nutritional content, and harvesting. RESULTS: In this study, we compared two genetic strains of BSF larvae (wild-type and laboratory-adapted line) in a bioconversion experiment with diverse types of food waste (homogeneous/heterogeneous; plant/meat) and we quantified the phenotypic plasticity. Our results demonstrate different plasticity in bioconversion performance, larval growth and larval nutrition between the two BSF lines. This difference may be attributed to the selective breeding the laboratory-adapted line has experienced. Notably, larval lipid content displayed little to no genetic variation for plasticity compared with larval protein and carbohydrate content. Despite variation in larval development, heterogeneous food wastes can produce better performance in bioconversion, larval growth, and larval nutrient content than homogeneous food waste. All-meat diets result in high larvae mortality but larval survival could be rescued by mixing meat with plant-based food wastes. CONCLUSION: Overall, we suggest using mixed meals for BSF larvae feeding. Targeted breeding may be a promising strategy for the BSF industry but it is important to consider the selection effects on plasticity in larval nutrition carefully. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Lactiplantibacillus brownii sp. nov., a novel psychrotolerant species isolated from sauerkraut.

A Gram-stain-positive, rod-shaped, facultatively anaerobic and homofermentative strain, named WILCCON 0030T, was isolated from sauerkraut (fermented cabbage) collected from a local market in the Moscow region of Russia. Comparative analyses based on 16S rRNA gene sequence similarity and whole genome relatedness indicated that strain WILCCON 0030T was most closely related to the type strains Lactiplantibacillus nangangensis NCIMB 15186T, Lactiplantibacillus daoliensis LMG 31171T and Lactiplantibacillus pingfangensis LMG 31176T. However, the average nucleotide identity and digital DNA-DNA hybridization prediction values with these closest relatives only ranged from 84.6 to 84.9 % and from 24.1 to 24.7 %, respectively, and were below the 95.0 and 70.0% thresholds for species delineation. Substantiated by further physiological and biochemical analyses, strain WILCCON 0030T represents a novel species within the genus Lactiplantibacillus for which we propose the name Lactiplantibacillus brownii sp. nov. (type strain WILCCON 0030T=DSM 116485T=LMG 33211T).

Whole-Genome Sequence of Ligilactobacillus faecis WILCCON 0062, Isolated from Feces of a Wild Boar (Sus scrofa).

We report the whole genome of a strain of Ligilactobacillus faecis. The complete circular chromosome and plasmid of strain WILCCON 0062 were obtained through a combination of short- and long-read sequencing and may be used to derive unprecedented insights into the genome-level phylogeny and functional capacities of Ligilactobacillus faecis.

Ligilactobacillus ubinensis sp. nov., a novel species isolated from the wild ferment of a durian fruit (Durio zibethinus).

A Gram-stain-positive, rod-shaped, non-spore-forming, catalase-negative, urease-negative, homofermentative and facultatively anaerobic strain, named WILCCON 0076T, was isolated from a wild ferment of pieces of a 'Kampung' durian fruit collected on the island of Ubin (Pulau Ubin), Singapore. The durian had fallen to the ground from a durian tree (Durio zibethinus), on which a group of long-tailed macaques had been observed picking and eating the fruits. Comparative analyses of 16S rRNA gene sequences indicated that WILCCON 0076T potentially represented a novel species within the genus Ligilactobacillus, with the most closely related type strain being Ligilactobacillus agilis DSM 20509T (16S rRNA gene sequence similarity of 97.2 %). Average nucleotide identity and digital DNA-DNA hybridization prediction values were only 86.0% and 18.9 %, respectively. On the basis of the results of a polyphasic approach that included phylogenomic, chemotaxonomic and morphological analyses, we propose a novel species with the name Ligilactobacillus ubinensis sp. nov. (type strain WILCCON 0076T=DSM 114293T=LMG 32698T).

Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach.

The lactobacilli identified to date encompass more than 270 closely related species that were recently reclassified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related and yet metabolically and regulatory distinct species, e.g., during monitoring of biotechnological processes or screening of samples of unknown composition. Current available methods, such as shotgun metagenomics or rRNA gene-based amplicon sequencing, have significant limitations (high cost, low resolution, etc.). Here, we generated a phylogeny of lactobacilli based on phenylalanyl-tRNA synthetase (pheS) genes and, from it, developed a high-resolution taxonomic framework which allows for comprehensive and confident characterization of the community diversity and structure of lactobacilli at the species level. This framework is based on a total of 445 pheS gene sequences, including sequences of 276 validly described species and subspecies (of a total of 282, including the proposed L. timonensis species and the reproposed L. zeae species; coverage of 98%), and allows differentiation between 265 species-level clades of lactobacilli and the subspecies of L. sakei The methodology was validated through next-generation sequencing of mock communities. At a sequencing depth of ∼30,000 sequences, the minimum level of detection was approximately 0.02 pg per µl DNA (equaling approximately 10 genome copies per µl template DNA). The pheS approach, along with parallel sequencing of partial 16S rRNA genes, revealed considerable diversity of lactobacilli and distinct community structures across a broad range of samples from different environmental niches. This novel complementary approach may be applicable to industry and academia alike.IMPORTANCE Species formerly classified within the genera Lactobacillus and Pediococcus have been studied extensively at the genomic level. To accommodate their exceptional functional diversity, the over 270 species were recently reclassified into 26 distinct genera. Despite their relevance to both academia and industry, methods that allow detailed exploration of their ecology are still limited by low resolution, high cost, or copy number variations. The approach described here makes use of a single-copy marker gene which outperforms other markers with regard to species-level resolution and availability of reference sequences (98% coverage). The tool was validated against a mock community and used to address diversity of lactobacilli and community structure in various environmental matrices. Such analyses can now be performed at a broader scale to assess and monitor the assembly, structure, and function of communities of lactobacilli at the species level (and, in some cases, even at the subspecies level) across a wide range of academic and commercial applications.

Dynamic shifts in chromatin states differentially mark the proliferative basal cells and terminally differentiated cells of the developing epidermis.

Post-translational modifications on nucleosomal histones represent a key epigenetic regulatory mechanism to mediate the complex gene expression, DNA replication, and cell cycle changes that occur in embryonic cells undergoing lineage specification, maturation, and differentiation during development. Here, we investigated the dynamics of 13 key histone marks in epidermal cells at three distinct stages of embryonic skin development and identified significant changes that corresponded with the maturation of the proliferative basal epidermal cells and terminally differentiated cells in the stratified layers. In particular, H3K4me3 and H3K27ac were accumulated and became more prominent in the basal cells at later stages of epidermal development, while H3K27me3 was found to be low in the basal cells but highly enriched in the differentiated suprabasal cell types. Constitutive heterochromatin marked by H4K20me3 was also significantly elevated in differentiated epidermal cells at late gestation stages, which exhibited a concomitant loss of H4K16 acetylation. These differential chromatin profiles were established in the embryonic skin by gestation day 15 and further amplified at E18 and in postnatal skin. Our results reveal the dynamic chromatin states that occur as epidermal progenitor cells commit to the lineage and differentiate into the different cells of the stratified epidermis and provide insight to the underlying epigenetic pathways that support normal epidermal development and homoeostasis.