Characterization and Simulation of Metagenomic Nanopore Sequencing Data with Meta-NanoSim

Background: Nanopore sequencing is crucial to metagenomic studies as its kilobase-long reads can contribute to resolving genomic structural differences among microbes. However, sequencing platform-specific challenges, including high base-call error rate, non-uniform read lengths, and the presence of chimeric artifacts, necessitate specifically designed analytical tools, such as microbial abundance estimation and metagenome assembly algorithms. When developing and testing bioinformatics tools and pipelines, the use of simulated datasets with characteristics that are true to the sequencing platform under evaluation is a cost-effective way to provide a ground truth and assess the performance in a controlled environment. Results: Here, we present Meta-NanoSim, a fast and versatile utility that characterizes and simulates the unique properties of nanopore metagenomic reads. It improves upon state-of-the-art methods on microbial abundance estimation through a base-level quantification algorithm. Meta-NanoSim can simulate complex microbial communities composed of both linear and circular genomes, and can stream reference genomes from online servers directly. Simulated datasets showed high congruence with experimental data in terms of read length, error profiles, and abundance levels. We demonstrate that Meta-NanoSim simulated data can facilitate the development of metagenomic algorithms and guide experimental design through a metagenome assembly benchmarking task. Conclusions: The Meta-NanoSim characterization module investigates read features including chimeric information and abundance levels, while the simulation module simulates large and complex multi-sample microbial communities with different abundance profiles. All trained models and the software are freely accessible at Github: https://github.com/bcgsc/NanoSim .

Spatial Meta-transcriptomes of human and murine intestines

We developed an analysis pipeline that can extract microbial sequences from Spatial Transcriptomic data and assign taxonomic labels to them, generating a spatial microbial abundance matrix in addition to the default host expression one, enabling simultaneous analysis of host expression and microbial distribution. We applied it on both human and murine intestinal datasets and validated the spatial microbial abundance information with alternative assays. Finally, we present a few biological insights that can be gained from this novel data. In summary, this proof of concept work demonstrated the feasibility of Spatial Meta-transcriptomic analysis, and pave the way for future experimental optimization.

Holo-Transcriptome Sequences from the Tropical Marine Sponge Cinachyrella alloclada

Marine sponge transcriptomes are underrepresented in current databases. Furthermore, only two sponge genomes are available for comparative studies. Here we present the assembled and annotated holo-transcriptome of the common Florida reef sponge from the species Cinachyrella alloclada. After Illumina high throughput sequencing, the data assembled using Trinity v2.5 confirmed a highly symbiotic organism, with the complexity of high microbial abundance (HMA) sponges. This dataset is enriched in poly-A selected eukaryotic, rather than microbial transcripts. Overall, 39,813 transcripts with verified sponge sequence homology coded for 8,496 unique proteins. The average sequence length was found to be 946 bp with an N50 sequence length of 1290 bp. Overall, the sponge assembly resulted in a GC content of 51.04%, which is within the range of GC bases in a eukaryotic transcriptome. BUSCO scored completeness analysis revealed a completeness of 60.3% and 60.1% based on the Eukaryota and Metazoa databases, respectively. Overall, this study points to an overarching goal of developing the Cinachyrella alloclada sponge as a useful new experimental model organism.

Effect of Nitrogen Addition on Soil Microbial Functional Gene Abundance and Community Diversity in Permafrost Peatland

Nitrogen is the limiting nutrient for plant growth in peatland ecosystems. Nitrogen addition significantly affects the plant biomass, diversity and community structure in peatlands. However, the response of belowground microbe to nitrogen addition in peatland ecosystems remains largely unknown. In this study, we performed long-term nitrogen addition experiments in a permafrost peatland in the northwest slope of the Great Xing’an Mountains. The four nitrogen addition treatments applied in this study were 0 g N·m−2·year−1 (CK), 6 g N·m−2·year−1 (N1), 12 g N·m−2·year−1 (N2), and 24 g N·m−2·year−1 (N3). Effects of nitrogen addition over a period of nine growing seasons on the soil microbial abundance and community diversity in permafrost peatland were analyzed. The results showed that the abundances of soil bacteria, fungi, archaea, nitrogen-cycling genes (nifH and b-amoA), and mcrA increased in N1, N2, and N3 treatments compared to CK. This indicated that nitrogen addition promoted microbial decomposition of soil organic matter, nitrogen fixation, ammonia oxidation, nitrification, and methane production. Moreover, nitrogen addition altered the microbial community composition. At the phylum level, the relative abundance of Proteobacteria increased significantly in the N2 treatment. However, the relative abundances of Actinobacteria and Verrucifera in the N2 treatment and Patescibacteria in the N1 treatment decreased significantly. The heatmap showed that the dominant order composition of soil bacteria in N1, N2, and N3 treatments and the CK treatment were different, and the dominant order composition of soil fungi in CK and N3 treatments were different. The N1 treatment showed a significant increase in the Ace and Chao indices of bacteria and Simpson index of fungi. The outcomes of this study suggest that nitrogen addition altered the soil microbial abundance, community structure, and diversity, affecting the soil microbial carbon and nitrogen cycling in permafrost peatland. The results are helpful to understand the microbial mediation on ecological processes in response to N addition.

Differences in the Structural Components Influence the Pumping Capacity of Marine Sponges

Marine sponges are important sessile, benthic filter feeders with a body plan designed to pump water efficiently. The sponge body plan generally consists of mineral spicules, gelatinous mesohyl, and the pores and canals of the aquiferous system. These structural components have stark differences in compressibility, mass, and volume; therefore, their proportion and distribution are likely to affect sponge morphology, anatomy, contraction, and finally the pumping capacity. We examined seven demosponge species (from high spicule skeleton contents to no spicules) commonly found along the central west coast of India for structural components, such as total inorganic contents (spicule skeleton and foreign inclusions), body density, porosity, and mesohyl TEM for the high microbial abundance/low microbial abundance status. Additionally, we estimated the sponge pumping rate by measuring the excurrent velocity, the abundance of individual pumping units and cells, i.e., choanocyte chambers and choanocytes, and also carried out a morphometric analysis of aquiferous structures. The excurrent velocity and the oscular flow rates showed a positive relationship with the oscular crosssectional area for all the study species. The inorganic spicule contents by their weight as well as volume formed a major component of tissue density and higher proportions of spicules were associated with reduced aquiferous structures and lower pumping rate. The ash mass% and the ash free dry weight (AFDW %) in the sponge dry mass showed separate and distinct associations with aquiferous system variables. For example, the number of choanocytes per chamber showed a wide difference between the studied species ranging from 35.02 ± 2.44 (C. cf. cavernosa) to 120.35 ± 8.98 (I. fusca) and had a significant positive relationship with AFDW% and a negative relationship with ash mass%. This study indicates that the differences in the proportions of structural components are closely related to sponge gross morphology, anatomy, and probably body contractions, factors that influence the sponge pumping capacity.