Additional file 1 of VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution

Additional file 1

Additional file 1 of ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently

Additional file 1. Fig. S1. The detailed workflow of the pipeline ASAP 2. The pipeline first imports organized input data as QZA, which are then used for demultiplexing (if applicable). The single-sample sequences are then denoised and feature tables are generated. Multiple projects are then merged to one feature table and a feature sequence file which are used in the downstream analysis. The file naming of each supported data formats are listed at left side, with some examples of QIIME 2 tutorial. The detailed processing and commands used were shown. For the data format codes, fq represents FASTQ; Mu represents multiplexed; De represents demultiplexed; Bi represents barcodeinside; Bo represents barcode-outside; Pe represents paired-end; Se represents single-end

Gut microbiota of Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis) responses to habitat change during translocations: clues to conservation management

High-throughput sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions were used to explore the diversity and composition of gut bacterial and fungal communities of Yangtze finless porpoises.<br

Internalization of myriocin involved in energy and affected expression of genes and proteins in the endocytosis pathway in <i>Fusarium oxysporum</i> f. sp. <i>niveum</i>

Myriocin, isolated from Bacillus amyloliquefaciens LZN01, can inhibit the growth of Fusarium oxysporum f. sp. niveum (Fon) by inducing membrane damage and targeting intracellular molecules. In the present study, the mechanism of myriocin entry into Fon cells was investigated. Fluorescence images demonstrated that internalization of myriocin was decreased by low temperature, NaN3 and Brefeldin A. The mechanism of myriocin entry into Fon cells was revealed by analyses of transcriptome and proteome. A total of 422 common differentially expressed genes (DEGs) were identified. Most of DEGs were assigned to transport and catabolism, folding, sorting and degradation, and enrichment analysis of some DEGs was closely related to transmembrane transport and vesicle transport. The combined analysis between the transcriptome and proteome showed that the expression levels of some related genes and proteins, mainly those related to oxidative phosphorylation, ABC transporters, micro chromosome maintenance protein, adaptor proteins etc., were affected. The DEGs were further verified by reverse transcription quantitative polymerase chain reaction (RT-qPCR). In conclusion, myriocin’s entry into Fon cells depended partially on energy and involved endocytosis, and the expression of certain genes and proteins was affected.</p

Additional file 2: of Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment

List of PTMs. (XLSX 696 kb

Additional file 1: Table S1. of Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment

Features of the assembled metagenomes and binned draft genomes. Table S2. Conserved single-copy protein-coding genes for the estimation of genome completeness. The numbers of the 139 single copy genes in Nitrospirae bacterium sp. nov were compared with that in closely related genomes. Table S3. Numbers of genes involved in carbohydrate metabolism, nitrogen metabolism, and sulfur metabolism in Nitrospirae bacterium sp. nov and the reference genomes. Figure S1. Work flow of the present study. Three samples were collected decimeters apart: one for the metagenomic sequencing, protein database construction, and genome binning and two for the metaproteomic and PTM analyses. Figure S2. A Venn diagram showing the overlaps between identified proteins (a) and PTMs (b) in the two metaproteomic samples. Figure S3. Alignments of partial F-type-ATPase protein sequences to show the PTM sites. Figure S4. Phylogenetic organization of the Nitrospirae bacterium sp. nov strain and closely related Nitrospirae strains based on 16S rRNA sequences (~1400 bp). Figure S5. Phylogenetic organization of the Nitrospirae bacterium sp. nov strain and Nitrospirae strains based on concatenated single-copy genes. (DOC 1298 kb

Additional file 1: of De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish

Table S1. Codon usage among Aldrovandia affinis, Astyanax mexicanus, Gadus morhua and Xiphophorus maculatus. Table S2. A complete list of positively selected genes in Aldrovandia affinis. Figure S1. Statistics of assembly contigs length. (DOCX 68 kb

Biodegradation of Polyethylene and Plastic Mixtures in Mealworms (Larvae of <i>Tenebrio molitor</i>) and Effects on the Gut Microbiome

Recent studies have demonstrated the ability for polystyrene (PS) degradation within the gut of mealworms (<i>Tenebrio molitor</i>). To determine whether plastics may be broadly susceptible to biodegradation within mealworms, we evaluated the fate of polyethylene (PE) and mixtures (PE + PS). We find that PE biodegrades at comparable rates to PS. Mass balances indicate conversion of up 49.0 ± 1.4% of the ingested PE into a putative gas fraction (CO₂). The molecular weights (<i>M</i>_n) of egested polymer residues decreased by 40.1 ± 8.5% in PE-fed mealworms and by 12.8 ± 3.1% in PS-fed mealworms. NMR and FTIR analyses revealed chemical modifications consistent with degradation and partial oxidation of the polymer. Mixtures likewise degraded. Our results are consistent with a nonspecific degradation mechanism. Analysis of the gut microbiome by next-generation sequencing revealed two OTUs (<i>Citrobacter</i> sp. and <i>Kosakonia</i> sp.) strongly associated with both PE and PS as well as OTUs unique to each plastic. Our results suggest that adaptability of the mealworm gut microbiome enables degradation of chemically dissimilar plastics

DataSheet_1_The effects of human care on the blowhole and gut microbiotas of two cohabiting dolphin species based on a year-round surveillance.docx

Understanding the effects of human care on the dynamics of the host-associated microbiota is critical for the health management of dolphins living in an aquarium. Yet this aspect remains relatively unexplored. Here, by utilizing 16S rRNA gene sequencing, we profiled the blowhole and gut bacterial communities of two bottlenose dolphins (Tursiops truncatus) and a Chinese white dolphin (Sousa chinensis) reared in the same indoor pool, based on year-round surveillance. In addition, we compared these dolphin microbiotas with those previously published datasets from wild dolphins. Our results showed that both the blowhole and the gut of the two dolphin species under human care shared a more similar microbiome than members of the same dolphin species across different habitats (human care vs wild). However, the effects of human care on the dolphin microbiome from the two body sites varied. In the aquarium, bacterial alpha diversities differed significantly between the two body sites, and the seasonal stability of the bacterial community was more evident in the gut than in the blowhole. Additionally, the blowhole bacterial composition and the predicted functional capacity from the two dolphin species showed differences and were less convergent than their gut microbiota over a decade-long cohabitation. Further analyses showed that heterogeneous and homogeneous selections (i.e., deterministic processes) contributed more to the blowhole than to the gut bacterial communities, while a dispersal limitation (i.e., a stochastic process) was more important for the gut microbiota. The present study provides the first comparative evidence that the gut microbiota may be more plastic in response to the human care environment than the blowhole microbiota. This improves our understanding of dolphin health management under human care and helps to predict their microbial responses to environmental changes.</p

Additional file 3: of The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

Sequence read numbers of the bacterial OTUs profiling (sequenced on a MiSeq PE250 sequencer at a depth of 29,718 sequences per sample). (XLS 882 kb