Highlights d The gut virome is highly unique to each individual and dominated by bacteriophages d Gut microbiome diversity, within and between subjects, is mirrored in their viromes d These patterns of diversity are driven by bacteriophages, not by eukaryotic viruses d Microbiome abundances and diversity are predictive of virome richness and diversity

This work reports the development of GenSeed-HMM, a program that implements seed-driven progressive assembly, an approach to reconstruct specific sequences from unassembled data, starting from short nucleotide or protein seed sequences or profile Hidden Markov Models (HMM). The program can use any one of a number of sequence assemblers. Assembly is performed in multiple steps and relatively few reads are used in each cycle, consequently the program demands low computational resources. As a proof-of-concept and to demonstrate the power of HMM-driven progressive assemblies, GenSeed-HMM was applied to metagenomic datasets in the search for diverse ssDNA bacteriophages from the recently described Alpavirinae subfamily. Profile HMMs were built using Alpavirinae-specific regions from multiple sequence alignments (MSA) using either the viral protein 1 (VP1; major capsid protein) or VP4 (genome replication initiation protein). These profile HMMs were used by GenSeed-HMM (running Newbler assembler) as seeds to reconstruct viral genomes from sequencing datasets of human fecal samples. All contigs obtained were annotated and taxonomically classified using similarity searches and phylogenetic analyses. The most specific profile HMM seed enabled the reconstruction of 45 partial or complete Alpavirinae genomic sequences. A comparison with conventional (global) assembly of the same original dataset, using Newbler in a standalone execution, revealed that GenSeed-HMM outperformed global genomic assembly in several metrics employed. This approach is capable of detecting organisms that have not been used in the construction of the profile HMM, which opens up the possibility of diagnosing novel viruses, without previous specific information, constituting a de novo diagnosis. Additional applications include, but are not limited to, the specific assembly of extrachromosomal elements such as plastid and mitochondrial genomes from metagenomic data. Profile HMM seeds can also be used to reconstruct specific protein coding genes for gene diversity studies, and to determine all possible gene variants present in a metagenomic sample. Such surveys could be useful to detect the emergence of drug-resistance variants in sensitive environments such as hospitals and animal production facilities, where antibiotics are regularly used. Finally, GenSeed-HMM can be used as an adjunct for gap closure on assembly finishing projects, by using multiple contig ends as anchored seeds.

SUMMARYThe virome is one of the most variable components of the human gut microbiome. Within twin-pairs, viromes have been shown to be similar for infants but not for adults, indicating that as twins age and their environments and microbiomes diverge, so do their viromes. The degree to which the microbiome drives the virome’s vast diversity is unclear. Here, we examined the relationship between microbiome diversity and virome diversity in 21 adult monozygotic twin pairs selected for high or low microbiome concordance. Viromes derived from virus-like particles were unique to each subject, dominated by Caudovirales and Microviridae, and exhibited a small core that included crAssphage. Microbiome-discordant twins had more dissimilar viromes compared to microbiome-concordant twins, and the richer the microbiomes, the richer the viromes. These patterns were driven by the bacteriophages, not eukaryotic viruses. These observations support a strong role of the microbiome in patterning the virome.

The circular economy (CE) has been proposed as a potentially significant catalyst to enhance the current response to the global climate crisis. The objective of this study was to investigate the scientific literature of the research between climate change and CE adopting a knowledge mapping approach. Based on a total of 789 peer-reviewed publications extracted from Scopus, we found that research on climate change and CE is continually growing and interdisciplinary in nature. Europe notably leads scientific production. Keyword evolution shows that CE has been influenced by more lines of research than climate change. We also found that waste management is the CE approach most associated with climate change, mitigation is the climate action most impacted by CE, and food is the most reported greenhouse gas (GHG)-emitting material. However, there are knowledge gaps in the integration of the social dimension, the promotion of climate change adaptation, and the association of sustainable development goal (SDG) 13. Finally, we identified four potentially valuable directions for future studies: (i) CE practices, (ii) bioeconomy, (iii) climate and energy, and (iv) sustainability and natural resources, in which carbon recovery technologies, green materials, regional supply chains, circular agriculture models, and nature-based solutions are promising themes.

Viruses, far from being just parasites affecting hosts’ fitness, are major players in any microbial ecosystem. In spite of their broad abundance, viruses, in particular bacteriophages, remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be annotated by comparison with public databases. In order to shed some light into this genetic dark matter we expanded the search of orthologous groups as potential markers to viral taxonomy from bacteriophages and included eukaryotic viruses, establishing a set of 31,150 ViPhOGs (Eukaryotic Viruses and Phages Orthologous Groups). To do this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information, and used all annotated and predicted proteins to identify potential protein domains. The clustering of domains and unannotated regions into orthologous groups was done using cogSoft. Finally, we employed a random forest implementation to classify genomes into their taxonomy and found that the presence or absence of ViPhOGs is significantly associated with their taxonomy. Furthermore, we established a set of 1457 ViPhOGs that given their importance for the classification could be considered as markers or signatures for the different taxonomic groups defined by the ICTV at the order, family, and genus levels.