Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes

Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes

BACKGROUND

Members of the Planctomycetota phylum harbour an outstanding potential for carbohydrate degradation given the abundance and diversity of carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members of the Planctomycetia class have been characterised up to now, and little is known about the degrading capacities of the other Planctomycetota. Here, we present a comprehensive comparative analysis of all available planctomycetotal genome representatives and detail encoded carbohydrolytic potential across phylogenetic groups and different habitats.

RESULTS

Our in-depth characterisation of the available planctomycetotal genomic resources increases our knowledge of the carbohydrolytic capacities of Planctomycetota. We show that this single phylum encompasses a wide variety of the currently known CAZyme diversity assigned to glycoside hydrolase families and that many members encode a versatile enzymatic machinery towards complex carbohydrate degradation, including lignocellulose. We highlight members of the Isosphaerales, Pirellulales, Sedimentisphaerales and Tepidisphaerales orders as having the highest encoded hydrolytic potential of the Planctomycetota. Furthermore, members of a yet uncultivated group affiliated to the Phycisphaerales order could represent an interesting source of novel lytic polysaccharide monooxygenases to boost lignocellulose degradation. Surprisingly, many Planctomycetota from anaerobic digestion reactors encode CAZymes targeting algal polysaccharides - this opens new perspectives for algal biomass valorisation in biogas processes.

CONCLUSIONS

Our study provides a new perspective on planctomycetotal carbohydrolytic potential, highlighting distinct phylogenetic groups which could provide a wealth of diverse, potentially novel CAZymes of industrial interest.

Molecular unraveling of polysaccharide digestion in wood-feeding termites: A solid-state NMR perspective

Termites are among the most efficient organisms utilizing polysaccharides from wood and play a significant role in global carbon recycling, especially within tropical and subtropical ecosystems. Yet, the molecular details in polysaccharide degradation by termites remain largely unexplored. In this work, we have elucidated the shared and distinct molecular details in polysaccharides digestion by the higher termite Nasutitermes on poplar and the lower termite Cryptotermes on pine using high resolution solid-state nuclear magnetic resonance spectroscopy. For the first time, structural polymers are partitioned into the minor mobile and dominant rigid phases for individual examination. The mobile polysaccharides receive less structural impacts and exhibit greater digestibility compared to the rigid counterparts. While both termites effectively degrade cellulose, Nasutitermes significantly outperforms Cryptotermes in hemicellulose breakdown. In the rigid phase, cellulose is comprehensively degraded into a fragmented and more dynamically consistent structure; As Nasutitermes breaks down hemicellulose in a similar manner to cellulose, Cryptotermes selectively digests hemicellulose at its interfaces with cellulose. Additionally, crystalline cellulose undergoes selective degradation, and the digestion of amorphous cellulose might involve sugar chain detachment within microfibrils. Overall, our findings offer significant advancements and fresh perspectives on the polysaccharide digestion strategies of different termite lineages.

Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda

The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.

Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs

BACKGROUND

Sesarmid crabs dominate mangrove habitats as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory are not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove ecosystems. Although endogenous cellulase expressions were reported in crabs, it remains unknown if endogenous enzymes alone can complete the whole lignocellulolytic pathway, or if they also depend on the contribution from the intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach.

RESULTS

Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs with different dietary preferences revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, including predominantly carnivorous species, suggesting the crab gut microbiomes have lignocellulolytic capacity regardless of dietary preference. Microbial cellulase, hemicellulase and pectinase genes in herbivorous and detritivorous crabs were differentially more abundant when compared to omnivorous and carnivorous crabs, indicating the importance of gut symbionts in lignocellulose degradation and the enrichment of lignocellulolytic microbes in response to diet with higher lignocellulose content. Herbivorous and detritivorous crabs showed highly similar CAZyme composition despite dissimilarities in taxonomic profiles observed in both groups, suggesting a stronger selection force on gut microbiota by functional capacity than by taxonomy. The gut microbiota in herbivorous sesarmid crabs were also enriched with nitrogen reduction and fixation genes, implying possible roles of gut microbiota in supplementing nitrogen that is deficient in plant diet.

CONCLUSIONS

Endosymbiotic microbes play an important role in lignocellulose degradation in most crab species. Their abundance is strongly correlated with dietary preference, and they are highly enriched in herbivorous sesarmids, thus enhancing their capacity in digesting mangrove leaves. Dietary preference is a stronger driver in determining the microbial CAZyme composition and taxonomic profile in the crab microbiome, resulting in functional redundancy of endosymbiotic microbes. Our results showed that crabs implement a mixed mode of digestion utilizing both endogenous and microbial enzymes in lignocellulose degradation, as observed in most of the more advanced herbivorous invertebrates.

Change of termite hindgut metabolome and bacteria after captivity indicates the hindgut microbiota provides nutritional factors to the host

The gut-dwelling microbiota is an indispensable part of termites. It is influenced by a series of factors, such as diet and captivity. The objectives of this study were to study the metabolic functions of hindgut microbiota and to investigate the influence of captivity on the hindgut microbiota. The dampwood termite Hodotermopsis sjostedti was reared in the laboratory for 6 months. We conducted the metabolome analysis of the fat body from the freshly-collected workers (FBF), the hindgut fluid of the freshly-collected workers (HFF), and the hindgut fluid of laboratory-maintained workers. In addition, the 16S rRNA genes from the hindgut bacteria in the freshly-collected and laboratory-maintained workers were sequenced. According to our results, the concentrations of metabolites associated with amino acid biosynthesis, vitamin biosynthesis, fatty acid biosynthesis, and cofactor biosynthesis were higher in HFF compared with those in FBF, suggesting that the hindgut microbiota provides nutritional factors to the host. However, after captivity, the concentrations of metabolites in the hindgut associated with amino acid biosynthesis, nucleotide sugar metabolism, vitamin biosynthesis, and carbon metabolism decreased, while those associated with the steroid hormone biosynthesis and ovarian steroidogenesis increased. Meanwhile, the 16S amplicon study revealed that the abundance of certain bacteria changed after captivity, such as uncultured Termite Group 1 bacterium, Candidatus Symbiothrix dinenymphae, and unclassified Desulfovibrio. Our findings show that captivity influences the hindgut microbiota and shed light on the metabolic potential of the hindgut microbiota.

Gut diazotrophs in lagomorphs are associated with season but not altitude and host phylogeny

Invertebrates such as termites feeding on nutrient-poor substrate receive essential nitrogen by biological nitrogen fixation of gut diazotrophs. However, the diversity and composition of gut diazotrophs of vertebrates such as Plateau pikas living in nutrient-poor Qinghai-Tibet Plateau remain unknown. To fill this knowledge gap, we studied gut diazotrophs of Plateau pikas (Ochotona curzoniae) and its related species, Daurian pikas (Ochotona daurica), Hares (Lepus europaeus) and Rabbits (Oryctolagus cuniculus) by high-throughput amplicon sequencing methods. We analyzed whether the gut diazotrophs of Plateau pikas are affected by season, altitude, and species, and explored the relationship between gut diazotrophs and whole gut microbiomes. Our study showed that Firmicutes, Spirochaetes, and Euryarchaeota were the dominant gut diazotrophs of Plateau pikas. The beta diversity of gut diazotrophs of Plateau pikas was significantly different from the other three lagomorphs, but the alpha diversity did not show a significant difference among the four lagomorphs. The gut diazotrophs of Plateau pikas were the most similarly to that of Rabbits, followed by Daurian pikas and Hares, which was inconsistent with gut microbiomes or animal phylogeny. The dominant gut diazotrophs of the four lagomorphs may reflect their living environment and dietary habits. Season significantly affected the alpha diversity and abundance of dominant gut diazotrophs. Altitude had no significant effect on the gut diazotrophs of Plateau pikas. In addition, the congruence between gut microbiomes and gut diazotrophs was low. Our results proved that the gut of Plateau pikas was rich in gut diazotrophs, which is of great significance for the study of ecology and evolution of lagomorphs.

Taxonomic profiling of Nasutitermes takasagoensis microbiota to investigate the role of termites as vectors of bacteria linked to ironwood tree decline in Guam

The ironwood tree (Casuarina equisetifolia, family Casuarinaceae), an indigenous agroforestry species in Guam, has been threatened by ironwood tree decline (IWTD) since 2002. Formation of bacterial ooze by the wilt pathogen from the Ralstonia solanacearum species complex and wetwood bacteria (primarily Klebsiella species) has been linked to IWTD. In addition, termite infestation of trees was statistically associated with IWTD. Termites are known carriers of a diverse microbiome. Therefore, we hypothesized that termites could be vectors of bacteria linked to IWTD. To investigate the potential role of termites as pathogen vectors, we employed next-generation 16S rRNA gene sequencing to describe the bacteria diversity of Nasutitermes takasagoensis (Family Termitidae) workers collected from 42 ironwood trees of different disease stages in Guam in association with tree-, plot-, and location-related factors. Nasutitermes takasagoensis workers account for the majority of termite infestations of ironwood trees. The bacterial phyla composition of N. takasagoensis workers was typical for wood-feeding higher termites consisting mainly of Spirochaetes and Fibrobacteres. However, Ralstonia species were not detected and Klebsiella species were rare even in termites collected from trees infected with Ralstonia and wetwood bacteria. Feeding experiments suggested that termites prefer to consume wood with low pathogen content over wood with high pathogen load. Termites were able to ingest Ralstonia but Ralstonia could not establish itself in healthy termite bodies. We concluded that N. takasagoensis workers are not vectors for Ralstonia spp. or the bacterial endophytes associated with wetwood (Klebsiella, Pantoea, Enterobacter, Citrobacter, and Erwinia) that were previously observed in IWTD-infested trees. The bacterial diversity in termite samples was significantly influenced by various factors, including Tree Health, Site Management, Plot Average Decline Severity, Proportion of Dead Trees in the Plot, Proportion of Trees with Termite Damage in the Plot, Presence of Ralstonia, and Altitude.

Understanding the Role of Free-Living Bacteria in the Gut of the Lower Termite Coptotermes gestroi Based on Metagenomic DNA Analysis

Termites' digestive systems, particularly in lower termites with the presence of protozoa, are unique ecological niches that shelter a diverse microbiota with a variety of functions for the host and the environment. In 2012, the metagenomic DNA (5.4 Gb) of the prokaryotes that freely live in the gut of the lower termite Coptotermes gestroi were sequenced. A total of 125,431 genes were predicted and analyzed in order to mine lignocellulolytic genes. however, the overall picture of the structure, diversity, and function of the prokaryotic gut microbiota was not investigated. In the present study, these 125,431 genes were taxonomically classified by MEGAN and functionally annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and by the Carbohydrate-Active enZYmes (CAZy) and HMMER databases. As a result, 95,751 bacterial genes were classified into 35 phyla. The structure of the bacteria, typified by a high ratio of Firmicutes to Bacterioidetes, was distinct from the structure of the entirety of the bacteria in the lower or higher termites' guts. The archaea (533 genes) were distributed into 4 phyla, 10 classes, 15 orders, 21 families, 47 genera, and 61 species. Although freely living in the guts, the prokaryotic community was formed, developed, and adapted to exhibit unique interactions in order to perform mutual roles of benefit to their hosts. Methanobacteriales, accounting for 61% of the archaea symbionts, seem to play an important role in methanogenesis. Concomitantly, bacterial methanotrophs in the gut utilize methane and combine with other bacterial groups, including potential lignocellulolytic degraders, acetogens, sulfur bacteria, and nitrogen-recycling bacteria, to efficiently convert wood with little nitrogen into acetates via certain pathway modules specified by prokaryotes that freely live in the gut. This forms an important energy source for the termites. Furthermore, bacteria carry 2223 genes involved in the biosynthesis of 17 antibiotic groups. The gut bacteria also possess genes for the degradation of 18 toxic aromatic compounds, of which four are commercial pesticides against termites commonly used for the preservation of wooden constructions. Eight of the eighteen pathways were the first to be reported from the termite gut. Overall, this study sheds light on the roles of the freely living bacteria and archaea in the C. gestroi gut, providing evidence that the gut microbiome acts as the second host genome, contributing both nutrients and immunity to support the host's existence, growth, and development.

Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants

While genome sequencing has expanded our knowledge of symbiosis, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont-Ischyrobacter davidsoniae (Betaproteobacteria: Burkholderiales: Alcaligenaceae)-and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication. Through new genome sequencing, we also show that divergent I. davidsoniae lineages are conserved in their uricolytic and urea-generating capacities. With phylogenetically refined definitions of Ischyrobacter and separately domesticated Burkholderiales symbionts, our FISH microscopy revealed a distinct niche for I. davidsoniae, with dense populations at the anterior ileum. Being positioned at the site of host N-waste delivery, in vivo metatranscriptomics and metabolomics further implicate I. davidsoniae within a symbiont-autonomous N-recycling pathway. While encoding much of this pathway, I. davidsoniae expressed only a subset of the requisite steps in mature adult workers, including the penultimate step deriving urea from allantoate. The remaining steps were expressed by other specialized gut symbionts. Collectively, this assemblage converts inosine, made from midgut symbionts, into urea and ammonia in the hindgut. With urea supporting host amino acid budgets and cuticle synthesis, and with the ancient nature of other active N-recyclers discovered here, I. davidsoniae emerges as a central player in a conserved and impactful, multipartite symbiosis.

Impact of Wood Age on Termite Microbial Assemblages

The decomposition of wood and detritus is challenging to most macroscopic organisms due to the recalcitrant nature of lignocellulose. Moreover, woody plants often protect themselves by synthesizing toxic or nocent compounds which infuse their tissues. Termites are essential wood decomposers in warmer terrestrial ecosystems and, as such, they have to cope with high concentrations of plant toxins in wood. In this paper, we evaluated the influence of wood age on the gut microbial (bacterial and fungal) communities associated with the termites Reticulitermes flavipes (Rhinotermitidae) (Kollar, 1837) and Microcerotermes biroi (Termitidae) (Desneux, 1905). We confirmed that the secondary metabolite concentration decreased with wood age. We identified a core microbial consortium maintained in the gut of R. flavipes and M. biroi and found that its diversity and composition were not altered by the wood age. Therefore, the concentration of secondary metabolites had no effect on the termite gut microbiome. We also found that both termite feeding activities and wood age affect the wood microbiome. Whether the increasing relative abundance of microbes with termite activities is beneficial to the termites is unknown and remains to be investigated. IMPORTANCE Termites can feed on wood thanks to their association with their gut microbes. However, the current understanding of termites as holobiont is limited. To our knowledge, no studies comprehensively reveal the influence of wood age on the termite-associated microbial assemblage. The wood of many tree species contains high concentrations of plant toxins that can vary with their age and may influence microbes. Here, we studied the impact of Norway spruce wood of varying ages and terpene concentrations on the microbial communities associated with the termites Reticulitermes flavipes (Rhinotermitidae) and Microcerotermes biroi (Termitidae). We performed a bacterial 16S rRNA and fungal ITS2 metabarcoding study to reveal the microbial communities associated with R. flavipes and M. biroi and their impact on shaping the wood microbiome. We noted that a stable core microbiome in the termites was unaltered by the feeding substrate, while termite activities influenced the wood microbiome, suggesting that plant secondary metabolites have negligible effects on the termite gut microbiome. Hence, our study shed new insights into the termite-associated microbial assemblage under the influence of varying amounts of terpene content in wood and provides a groundwork for future investigations for developing symbiont-mediated termite control measures.

Integrated analysis of miRNA and mRNA expression profiles in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis

Insect gut microbiota has been reported to participate in regulating host multiple biological processes including metabolism and reproduction. However, the corresponding molecular mechanisms remain largely unknown. Recent studies suggest that microRNAs (miRNAs) are involved in complex interactions between the gut microbiota and the host. Here, we used next-generation sequencing technology to characterize miRNA and mRNA expression profiles and construct the miRNA-gene regulatory network in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis. A total of 3016 differentially expressed genes (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Based on the integrated analysis of miRNA and mRNA sequencing data, 229 negatively correlated miRNA-gene pairs were identified from the miRNA-mRNA network. Gene ontology enrichment analysis indicated that DEMs could target several genes involved in the metabolic process, oxidation-reduction process, oogenesis, and insulin signaling pathway. Finally, real-time quantitative polymerase chain reaction further verified the accuracy of RNA sequencing results. In conclusion, our study provides the profiles of miRNA and mRNA expressions under antibiotics treatment and provides an insight into the roles of miRNAs and their target genes in the interaction between the gut microbiota and its host.

A holobiont approach towards polysaccharide degradation by the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis

BACKGROUND

Termites are among the most successful insects on Earth and can feed on a broad range of organic matter at various stages of decomposition. The termite gut system is often referred to as a micro-reactor and is a complex structure consisting of several components. It includes the host, its gut microbiome and fungal gardens, in the case of fungi-growing higher termites. The digestive tract of soil-feeding higher termites is characterised by radial and axial gradients of physicochemical parameters (e.g. pH, O₂ and H₂ partial pressure), and also differs in the density and structure of residing microbial communities. Although soil-feeding termites account for 60% of the known termite species, their biomass degradation strategies are far less known compared to their wood-feeding counterparts.

RESULTS

In this work, we applied an integrative multi-omics approach for the first time at the holobiont level to study the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis. We relied on 16S rRNA gene community profiling, metagenomics and (meta)transcriptomics to uncover the distribution of functional roles, in particular those related to carbohydrate hydrolysis, across different gut compartments and among the members of the bacterial community and the host itself. We showed that the Labiotermes gut was dominated by members of the Firmicutes phylum, whose abundance gradually decreased towards the posterior segments of the hindgut, in favour of Bacteroidetes, Proteobacteria and Verrucomicrobia. Contrary to expectations, we observed that L. labralis gut microbes expressed a high diversity of carbohydrate active enzymes involved in cellulose and hemicelluloses degradation, making the soil-feeding termite gut a unique reservoir of lignocellulolytic enzymes with considerable biotechnological potential. We also evidenced that the host cellulases have different phylogenetic origins and structures, which is possibly translated into their different specificities towards cellulose. From an ecological perspective, we could speculate that the capacity to feed on distinct polymorphs of cellulose retained in soil might have enabled this termite species to widely colonise the different habitats of the Amazon basin.

CONCLUSIONS

Our study provides interesting insights into the distribution of the hydrolytic potential of the highly compartmentalised higher termite gut. The large number of expressed enzymes targeting the different lignocellulose components make the Labiotermes worker gut a relevant lignocellulose-valorising model to mimic by biomass conversion industries.

Can wood-feeding termites solve the environmental bottleneck caused by plastics? A critical state-of-the-art review

The abundance of synthetic polymers has become an ever-increasing environmental threat in the world. The excessive utilization of plastics leads to the accumulation of such recalcitrant pollutants in the environment. For example, during the COVID-19 pandemic, unprecedented demand for personal protective equipment (PPE) kits, face masks, and gloves made up of single-use items has resulted in the massive generation of plastic biomedical waste. As secondary pollutants, microplastic particles (<5 mm) are derived from pellet loss and degradation of macroplastics. Therefore, urgent intervention is required for the management of these hazardous materials. Physicochemical approaches have been employed to degrade synthetic polymers, but these approaches have limited efficiency and cause the release of hazardous metabolites or by-products into the environment. Therefore, bioremediation is a proper option as it is both cost-efficient and environmentally friendly. On the other hand, plants evolved lignocellulose to be resistant to destruction, whereas insects, such as wood-feeding termites, possess diverse microorganisms in their guts, which confer physiological and ecological benefits to their host. Plastic and lignocellulose polymers share a number of physical and chemical properties, despite their structural and recalcitrance differences. Among these similarities are a hydrophobic nature, a carbon skeleton, and amorphous/crystalline regions. Compared with herbivorous mammals, lignocellulose digestion in termites is accomplished at ordinary temperatures. This unique characteristic has been of great interest for the development of a plastic biodegradation approach by termites and their gut symbionts. Therefore, transferring knowledge from research on lignocellulosic degradation by termites and their gut symbionts to that on synthetic polymers has become a new research hotspot and technological development direction to solve the environmental bottleneck caused by synthetic plastic polymers.

SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes

Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM, GUNC), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Importantly, these additional MAGs showed no significant difference compared to the other ones in terms of completeness, contamination, genome size nor relative abundance. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.

SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes

Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.

Microbial gut diversity in four grasshopper species and its correlation with cellulose digestibility

Grasshoppers are common pests, and their intestinal microbes have coevolved with them. These microorganisms have varied community structures, and they participate in the nutritional absorption and metabolism of grasshoppers. Here, we describe the gut microbiota diversity of four species of grasshoppers, Oxya chinensis, Pararcyptera microptera meridionalis, Gastrimargus marmoratus, and Calliptamus abbreviatus. We constructed a 16S rDNA gene library and analyzed the digestibility of cellulose and hemicellulose in grasshoppers using moss black phenol and anthrone colorimetry. The grasshopper with the highest microbial diversity in the gut among the four species was Oxya chinensis, and there were no significant differences in gut microbial diversity between the two geographic collections of Oxya chinensis. The most dominant phyla of the four grasshopper gut microorganisms were Proteobacteria, Bacteroidetes, and Firmicutes, and the most dominant genus was Enterobacter. The gut microbiota features of the four grasshoppers were correlated with their cellulose and hemicellulose digestibility. There was a significant positive correlation with cellulose digestibility for Pantoea. A significant negative correlation was found with cellulose digestibility for Acinetobacter, Enterococcus, Citrobacter, Serratia. A significant negative correlation was found with hemicellulose digestibility for Pantoea. This study contributes to the understanding of the structural composition of different species of grasshoppers gut microbiota, which may be useful for developing grasshopper digestive tracts as bioreactors for cellulose decomposition, improving the decomposition and utilization of agricultural straw, producing clean biomass energy, and processing biologically derived products.

CAZyme from gut microbiome for efficient lignocellulose degradation and biofuel production

Over-exploitation and energy security concerns of the diminishing fossil fuels is a challenge to the present global economy. Further, the negative impact of greenhouse gases released using conventional fuels has led to the need for searching for alternative biofuel sources with biomass in the form of lignocellulose coming up as among the potent candidates. The entrapped carbon source of the lignocellulose has multiple applications other than biofuel generation under the biorefinery approach. However, the major bottleneck in using lignocellulose for biofuel production is its recalcitrant nature. Carbohydrate Active Enzymes (CAZymes) are enzymes that are employed for the disintegration and consumption of lignocellulose biomass as the carbon source for the production of biofuels and bio-derivatives. However, the cost of enzyme production and their stability and catalytic efficiency under stressed conditions is a concern that hinders large-scale biofuel production and utilization. Search for novel CAZymes with superior activity and stability under industrial condition has become a major research focus in this area considering the fact that the most conventional CAZymes has low commercial viability. The gut of plant-eating herbivores and other organisms is a potential source of CAZyme with high efficiency. The review explores the potential of the gut microbiome of various organisms in the production of an efficient CAZyme system and the challenges in using the biofuels produced through this approach as an alternative to conventional biofuels.

Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats

Bamboo rats (Rhizomys pruinosus) are among the few mammals that lives on a bamboo-based diet which is mainly composed of lignocellulose. However, the mechanisms of adaptation of their gut microbiome and metabolic systems in the degradation of lignocellulose are largely unknown. Here, we conducted a multi-omics analysis on bamboo rats to investigate the interaction between their gut microbiomes and metabolic systems in the pre- and post-weaning periods, and observed significant relationships between dietary types, gut microbiome, serum metabolome and host gene expression. For comparison, published gut microbial data from the famous bamboo-eating giant panda (Ailuropoda melanoleuca) were also used for analysis. We found that the adaptation of the gut microbiome of the bamboo rat to a lignocellulose diet is related to a member switch in the order Bacteroidales from family Bacteroidaceae to family Muribaculaceae, while for the famous bamboo-eating giant panda, several aerobes and facultative anaerobes increase after weaning. The conversion of bacteria with an increased relative abundance in bamboo rats after weaning enriched diverse carbohydrate-active enzymes (CAZymes) associated with lignocellulose degradation and functionally enhanced the biosynthesis of amino acids and B vitamins. Meanwhile, the circulating concentration of short-chain fatty acids (SCFAs) derived metabolites and the metabolic capacity of linoleic acid in the host were significantly elevated. Our findings suggest that fatty acid metabolism, including linoleic acid and SCFAs, are the main energy sources for bamboo rats in response to the low-nutrient bamboo diet.

Oxidative cleavage of polysaccharides by a termite-derived superoxide dismutase boosts the degradation of biomass by glycoside hydrolases

Wood-feeding termites effectively degrade plant biomass through enzymatic degradation. Despite their high efficiencies, however, individual glycoside hydrolases isolated from termites and their symbionts exhibit anomalously low effectiveness in lignocellulose degradation, suggesting hereto unknown enzymatic activities in their digestome. Herein, we demonstrate that an ancient redox-active enzyme encoded by the lower termite Coptotermes gestroi, a Cu/Zn superoxide dismutase (CgSOD-1), plays a previously unknown role in plant biomass degradation. We show that CgSOD-1 transcripts and peptides are up-regulated in response to an increased level of lignocellulose recalcitrance and that CgSOD-1 localizes in the lumen of the fore- and midguts of C. gestroi together with termite main cellulase, CgEG-1-GH9. CgSOD-1 boosts the saccharification of polysaccharides by CgEG-1-GH9. We show that the boosting effect of CgSOD-1 involves an oxidative mechanism of action in which CgSOD-1 generates reactive oxygen species that subsequently cleave the polysaccharide. SOD-type enzymes constitute a new addition to the growing family of oxidases, ones which are up-regulated when exposed to recalcitrant polysaccharides, and that are used by Nature for biomass degradation.

Turtle ants harbor metabolically versatile microbiomes with conserved functions across development and phylogeny

Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. However, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through (meta)genomic screening and in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant dietary fibers and energy-generating fermentation. Additionally, several members of the specialized adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers. Symbionts from both life stages have the genomic capacity to recycle nitrogen and synthesize amino acids and B-vitamins. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae may aid colony digestion and contribute to colony-wide nitrogen, B-vitamin and energy budgets. In addition, the conserved nature of the digestive capacities among adult-associated symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 45 million years of residency.

The functional evolution of termite gut microbiota

BACKGROUND

Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species but remains largely unknown in other taxa. We intend to fill this gap and provide a global understanding of the functional evolution of termite gut microbiota.

RESULTS

We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that essential nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways.

CONCLUSIONS

Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ~ 150 million years ago. Therefore, the "world's smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception. Video Abstract.

Dietary Fiber Influences Bacterial Community Assembly Processes in the Gut Microbiota of Durco × Bamei Crossbred Pig

Several studies have shown that dietary fiber can significantly alter the composition and structure of the gut bacterial community in humans and mammals. However, few researches have been conducted on the dynamics of the bacterial community assembly across different graded levels of dietary fiber in different gut regions. To address this, 24 Durco × Bamei crossbred pigs were randomly assigned to four experimental chows comprising graded levels of dietary fiber. Results showed that the α-and β-diversity of the bacterial community was significantly different between the cecum and the jejunum. Adding fiber to the chow significantly increased the α-diversity of the bacterial community in the jejunum and cecum, while the β-diversity decreased. The complexity of the bacterial network increased with the increase of dietary fiber in jejunal content samples, while it decreased in cecal content samples. Furthermore, we found that stochastic processes governed the bacterial community assembly of low and medium dietary fiber groups of jejunal content samples, while deterministic processes dominated the high fiber group. In addition, deterministic processes dominated all cecal content samples. Taken together, the variation of gut community composition and structure in response to dietary fiber was distinct in different gut regions, and the dynamics of bacterial community assembly across the graded levels of dietary fiber in different gut regions was also distinct. These findings enhanced our knowledge on the bacterial community assembly processes in gut ecosystems of livestock.

Molecular Rationale of Insect-Microbes Symbiosis-From Insect Behaviour to Mechanism

Insects nurture a panoply of microbial populations that are often obligatory and exist mutually with their hosts. Symbionts not only impact their host fitness but also shape the trajectory of their phenotype. This co-constructed niche successfully evolved long in the past to mark advanced ecological specialization. The resident microbes regulate insect nutrition by controlling their host plant specialization and immunity. It enhances the host fitness and performance by detoxifying toxins secreted by the predators and abstains them. The profound effect of a microbial population on insect physiology and behaviour is exploited to understand the host–microbial system in diverse taxa. Emergent research of insect-associated microbes has revealed their potential to modulate insect brain functions and, ultimately, control their behaviours, including social interactions. The revelation of the gut microbiota–brain axis has now unravelled insects as a cost-effective potential model to study neurodegenerative disorders and behavioural dysfunctions in humans. This article reviewed our knowledge about the insect–microbial system, an exquisite network of interactions operating between insects and microbes, its mechanistic insight that holds intricate multi-organismal systems in harmony, and its future perspectives. The demystification of molecular networks governing insect–microbial symbiosis will reveal the perplexing behaviours of insects that could be utilized in managing insect pests.

Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion

Microbial consortia efficiently degrade complex biopolymers found in the organic fraction of municipal solid waste (OFMSW). Through enzyme production and division of labor during anaerobic digestion, microbial communities break down recalcitrant polymers and make fermentation products, including methane. However, microbial communities remain underutilized for waste degradation as it remains difficult to characterize and predict microbial interactions during waste breakdown, especially as cultivation conditions change drastically throughout anaerobic digestion. This review discusses recent progress and opportunities in cultivating natural and engineered consortia for OFMSW hydrolysis, including how recalcitrant substrates are degraded by enzymes as well as the critical factors that govern microbial interactions and culture stability. Methods to measure substrate degradation are also reviewed, and we demonstrate the need for increased standardization to enable comparisons across different environments.

GC/TOF-MS-Based Metabolomics Reveals Altered Metabolic Profiles in Wood-Feeding Termite Coptotermes formosanus Shiraki Digesting the Weed Mikania micrantha Kunth

Effective approaches to exploiting the biomass of the abundant invasive weed Mikania micrantha Kunth are limited. Termites have been a focus of significant attention as mediators of biomass-processing owing to their ability to digest lignocellulose. Here, the GC/TOF-MS approach was employed to assess the effects of a diet composed of M. micrantha leaves on Coptotermes formosanus workers, with the growth performance of these workers also being assessed. The workers increased their dietary intake when fed M. micrantha leaves, with a concomitant gradual increase in mortality rate. A total of 62 differentially abundant metabolites and nine significantly affected pathways were found when comparing termites fed M. micrantha leaves to pinewood. Key metabolites, including carbohydrates, polyols, 4-hydroxyphenylacetic acid, and their related metabolic pathways, suggested that termites can digest and utilize M. micrantha-derived lignocellulose. However, changes in the tryptophan metabolism, tyrosine metabolism, and sphingolipid metabolism suggest an adverse effect of M. micrantha leaves on antioxidant activity and signal transduction in termites. Overall, this study identified the key metabolites and pathways associated with the response of these termites to dietary changes and the effect of M. micrantha on termites.

The role of gut mycobiome in health and diseases

The gut microbiome comprised of microbes from multiple kingdoms, including bacteria, fungi, and viruses. Emerging evidence suggests that the intestinal fungi (the gut "mycobiome") play an important role in host immunity and inflammation. Advances in next generation sequencing methods to study the fungi in fecal samples and mucosa tissues have expanded our understanding of gut fungi in intestinal homeostasis and systemic immunity in health and their contribution to different human diseases. In this review, the current status of gut mycobiome in health, early life, and different diseases including inflammatory bowel disease, colorectal cancer, and metabolic diseases were summarized.

Metagenome-assembled genome of a Chitinophaga sp. and its potential in plant biomass degradation, as well of affiliated Pandoraea and Labrys species

The prospection of new degrading enzymes of the plant cell wall has been the subject of many studies and is fundamental for industries, due to the great biotechnological importance of achieving a more efficient depolymerization conversion from plant polysaccharides to fermentable sugars, which are useful not only for biofuel production but also for various bioproducts. Thus, we explored the shotgun metagenome data of a bacterial community (CB10) isolated from sugarcane bagasse and recovered three metagenome-assembled genomes (MAGs). The genomic distance analyses, along with phylogenetic analysis, revealed the presence of a putative novel Chitinophaga species, a Pandoraea nosoerga, and Labrys sp. isolate. The isolation process for each one of these bacterial lineages from the community was carried out in order to relate them with the MAGs. The recovered draft genomes have reasonable completeness (72.67-100%) and contamination (0.26-2.66%) considering the respective marker lineage for Chitinophaga (Bacteroidetes), Pandoraea (Burkholderiales), and Labrys (Rhizobiales). The in-vitro assay detected cellulolytic activity (endoglucanases) only for the isolate Chitinophaga, and its genome analysis revealed 319 CAZymes, of which 115 are classified as plant cell wall degrading enzymes, which can act in fractions of hemicellulose and pectin. Our study highlights the potential of this Chitinophaga isolate provides several plant-polysaccharide-degrading enzymes.

A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides

Background

Lignocellulose is a renewable and enormous biomass resource, which can be degraded efficiently by a range of cocktails of carbohydrate-active enzymes secreted by termite gut symbiotic bacteria. There is an urgent need to find enzymes with novel characteristics for improving the conversion processes in the production of lignocellulosic-based products. Although various studies dedicated to the genus Cellulosimicrobium as gut symbiont, genetic potential related to plant biomass-acting enzymes and exopolysaccharides production has been fully untapped to date.

Methods

The cellulolytic bacterial strain MP1 was isolated from termite guts and identified to the species level by phenotypic, phylogenetic, and genomic analysis. To further explore genes related to cellulose and hemicellulose degradation, the draft genome of strain MP1 was obtained by using whole-genome sequencing, assembly, and annotation through the Illumina platform. Lignocellulose degrading enzymes and levan production in the liquid medium were also examined to shed light on bacterial activities.

Results

Among 65 isolates obtained, the strain MP1 was the most efficient cellulase producer with cellulase activity of 0.65 ± 0.02 IU/ml. The whole genome analysis depicted that strain MP1 consists of a circular chromosome that contained 4,580,223 bp with an average GC content of 73.9%. The genome comprises 23 contigs including 67 rRNA genes, three tRNA genes, a single tmRNA gene, and 4,046 protein-coding sequences. In support of the phenotypic identification, the 16S rRNA gene sequence, average nucleotide identity, and whole-genome-based taxonomic analysis demonstrated that the strain MP1 belongs to the species Cellulosimicrobium cellulans. A total of 30 genes related to the degradation of cellulases and hemicellulases were identified in the C. cellulans MP1 genome. Of note, the presence of sacC1-levB-sacC2-ls operon responsible for levan and levan-type fructooligosaccharides biosynthesis was detected in strain MP1 genome, but not with closely related C. cellulans strains, proving this strain to be a potential candidate for further studies. Endoglucanases, exoglucanases, and xylanase were achieved by using cheaply available agro-residues such as rice bran and sugar cane bagasse. The maximum levan production by C. cellulans MP1 was 14.8 ± 1.2 g/l after 20 h of cultivation in media containing 200 g/l sucrose. To the best of our knowledge, the present study is the first genome-based analysis of a Cellulosimicrobium species which focuses on lignocellulosic enzymes and levan biosynthesis, illustrating that the C. cellulans MP1 has a great potential to be an efficient platform for basic research and industrial exploitation.

All creatures great and small: celebrating the microbiome

The collection of bacteria, fungi, and other microbes that form microbiota play an important role in both human and environmental health. In recognition of World Microbiome Day, we have curated a Collection of articles, news and commentary to celebrate the diversity of microbiome research published at Communications Biology , and highlight exciting new avenues for the field.

Unlocking the potential of insect and ruminant host symbionts for recycling of lignocellulosic carbon with a biorefinery approach: a review

Uprising fossil fuel depletion and deterioration of ecological reserves supply have led to the search for alternative renewable and sustainable energy sources and chemicals. Although first generation biorefinery is quite successful commercially in generating bulk of biofuels globally, the food versus fuel debate has necessitated the use of non-edible feedstocks, majorly waste biomass, for second generation production of biofuels and chemicals. A diverse class of microbes and enzymes are being exploited for biofuels production for a series of treatment process, however, the conversion efficiency of wide range of lignocellulosic biomass (LCB) and consolidated way of processing remains challenging. There were lot of research efforts in the past decade to scour for potential microbial candidate. In this context, evolution has developed the gut microbiota of several insects and ruminants that are potential LCB degraders host eco-system to overcome its host nutritional constraints, where LCB processed by microbiomes pretends to be a promising candidate. Synergistic microbial symbionts could make a significant contribution towards recycling the renewable carbon from distinctly abundant recalcitrant LCB. Several studies have assessed the bioprospection of innumerable gut symbionts and their lignocellulolytic enzymes for LCB degradation. Though, some reviews exist on molecular characterization of gut microbes, but none of them has enlightened the microbial community design coupled with various LCB valorization which intensifies the microbial diversity in biofuels application. This review provides a deep insight into the significant breakthroughs attained in enrichment strategy of gut microbial community and its molecular characterization techniques which aids in understanding the holistic microbial community dynamics. Special emphasis is placed on gut microbial role in LCB depolymerization strategies to lignocellulolytic enzymes production and its functional metagenomic data mining eventually generating the sugar platform for biofuels and renewable chemicals production.

Microbial enrichment and meta-omics analysis identify CAZymes from mangrove sediments with unique properties

Although lignocellulose is the most abundant and renewable natural resource for biofuel production, its use remains under exploration because of its highly recalcitrant structure. Its deconstruction into sugar monomers is mainly driven by carbohydrate-active enzymes (CAZymes). To develop highly efficient and fast strategies to discover biomass-degrading enzymes for biorefinery applications, an enrichment process combined with integrative omics approaches was used to identify new CAZymes. The lignocellulolytic-enriched mangrove microbial community (LignoManG) established on sugarcane bagasse (SB) was enriched with lignocellulolytic bacteria and fungi such as Proteobacteria, Bacteroidetes, Basidiomycota, and Ascomycota. These microbial communities were able to degrade up to 55 % of the total SB, indicating the production of lignocellulolytic enzymes. Metagenomic analysis revealed that the LignoManG harbors 18.042 CAZyme sequences such as of cellulases, hemicellulases, carbohydrate esterases, and lytic polysaccharide monooxygenase. Similarly, our metaproteomic analysis depicted several enzymes from distinct families of different CAZy families. Based on the LignoManG data, a xylanase (coldXynZ) was selected, amplified, cloned, expressed, and biochemically characterized. The enzyme displayed psicrofilic properties, with the highest activity at 15 °C, retaining 77 % of its activity when incubated at 0 °C. Moreover, molecular modeling in silico indicated that coldXynZ is composed of a TIM barrel, which is a typical folding found in the GH10 family, and displayed similar structural features related to cold-adapted enzymes. Collectively, the data generated in this study represent a valuable resource for lignocellulolytic enzymes with potential biotechnological applications.

Evaluation of cellulose degrading bacteria isolated from the gut-system of cotton bollworm, Helicoverpa armigera and their potential values in biomass conversion

Background

Cotton bollworm, Helicoverpa armigera is a widely distributed, devastating pest of over 200 crop plants that mainly consist of some cellulosic materials. Despite its economic importance as a pest, little is known about the diversity and community structure of gut symbiotic bacteria potentially functioned in cellulose digestion in different gut-sections of H. armigera. In view of this lacuna, we attempted to evaluate and characterize cellulose-degrading bacteria (CDB) from foregut, midgut, and hindgut -regions of H. armigera by using a culture-dependent approach.

Methodology

The symbiotic bacteria were isolated from different gut-systems of H. armigera by enrichment techniques using Carboxymethyl cellulose sodium salt (CMC) as carbon source. The isolated bacteria were purified and subsequently screened for cellulose-degradation by plate-based method to display the zones of CMC clearance around the colonies. The identification and phylogeny of the gut-bacteria were reconstructed by using 16S rRNA gene sequencing. Different enzymes such as endoglucanase, exoglucanase, β-glucosidase, and xylanase were assayed to determine the cellulolytic repertoire of the isolated bacteria.

Results

The enrichment of CDB and subsequent plate based screening methods resulted in isolation of 71 bacteria among which 54% of the bacteria were obtained from foregut. Among the isolated bacteria, 25 isolates showed discernible cellulose-degradation potential on CMC-agar plates. The phylogenetic analysis based on 16S rRNA gene amplification and sequencing affiliated these cellulolytic bacteria to two major phyla viz., Firmicutes and Proteobacteria. The members of the genus Klebsiella accounted for 39.43% of the total isolated bacteria while 31% of the Bacillus strains were enriched from hindgut region. The principal component analysis (PCA) further suggested that the members of Bacillus and Klebsiella together dominated the foregut and hindgut regions as they accounted for 68% of the total CDB. The four potential isolates selected on the basis of plate-based activities were further evaluated for their lignocellulases production by using various agricultural wastes as substrates. The PCA of the enzyme activities demonstrated that potential isolates majorly secreted endoglucanase and xylanase enzymes. Among the agro-wastes, multivariate analysis validated wheat husk (WH) and sugarcane bagasse (SCB) as most favorable substrates for xylanase and endoglucanase productions respectively. The overall findings suggest that H. armigera harbors diverse bacterial communities in different gut-sections that could assist the host in digestion processes, which may potentially serve as a valuable reservoir of some unique symbionts applied for biomass conversion in biofuel industry.

Diversity structure of the microbial communities in the guts of four neotropical termite species

The termite gut microbiome is dominated by lignocellulose degrading microorganisms. This study describes the intestinal microbiota of four Argentinian higher termite species with different feeding habits: Microcerotermes strunckii (hardwood), Nasutitermes corniger (softwood), Termes riograndensis (soil organic matter/grass) and Cornitermes cumulans (grass) by deep sequencing of amplified 16S rRNA and ITS genes. In addition, we have performed a taxonomic and gut community structure comparison incorporating into the analysis the previously reported microbiomes of additional termite species with varied diets. The bacterial phylum Spirochaetes was dominant in the guts of M. strunckii, N. corniger and C. cumulans, whereas Firmicutes predominated in the T. riograndensis gut microbiome. A single bacterial genus, Treponema (Spirochaetes), was dominant in all termite species, except for T. riograndensis. Both in our own sequenced samples and in the broader comparison, prokaryotic α-diversity was higher in the soil/grass feeders than in the wood feeders. Meanwhile, the β-diversity of prokaryotes and fungi was highly dissimilar among strict wood-feeders, whereas that of soil- and grass-feeders grouped more closely. Ascomycota and Basidiomycota were the only fungal phyla that could be identified in all gut samples, because of the lack of reference sequences in public databases. In summary, higher microbial diversity was recorded in termites with more versatile feeding sources, providing further evidence that diet, along with other factors (e.g., host taxonomy), influences the microbial community assembly in the termite gut.

The sum is greater than the parts: exploiting microbial communities to achieve complex functions

Multi-species microbial communities are ubiquitous in nature. The widespread prevalence of these communities is due to highly elaborated interactions among their members thereby accomplishing metabolic functions that are unattainable by individual members alone. Harnessing these communal capabilities is an emerging field in biotechnology. The rational intervention of microbial communities for the purpose of improved function has been facilitated in part by developments in multi-omics approaches, synthetic biology, and computational methods. Recent studies have demonstrated the benefits of rational interventions to human and animal health as well as agricultural productivity. Emergent technologies, such as in situ modification of complex microbial community and community metabolic modeling, represent an avenue to engineer sustainable microbial communities. In this opinion, we review relevant computational and experimental approaches to study and engineer microbial communities and discuss their potential for biotechnological applications.

Functional and structural characterization of a novel GH3 β-glucosidase from the gut metagenome of the Brazilian Cerrado termite Syntermes wheeleri

In this study, a GH3 family β-glucosidase (Bgl7226) from metagenomic sequences of the Syntermes wheeleri gut, a Brazilian Cerrado termite, was expressed, purified and characterized. The enzyme showed two optimum pHs (pH 7 and pH 10), and a maximum optimum temperature of about 40 °C using 4-Nitrophenyl β-D-glucopyranoside (pNPG) as substrate. Bgl7226 showed higher enzymatic activity at basic pH, but higher affinity (K_m) at neutral pH. However, at neutral pH the Bgl7226 enzyme showed higher catalytic efficiency (k_cat/K_m) for pNPG substrate. Predictive analysis about the enzyme structure-function relationship by sequence alignment suggested the presence of multi-domains and conserved catalytic sites. Circular dichroism results showed that the secondary structure composition of the enzyme is pH-dependent. Small conformational changes occurred close to the optimum temperature of 40 ^o C, and seem important for the highest activity of Bgl7226 observed at pH 7 and 10. In addition, the small transition in the unfolding curves close to 40 ^o C is typical of intermediates associated with proteins structured in several domains. Bgl7226 has significant β-glucosidase activity which could be attractive for biotechnological applications, such as plant roots detoxification; specifically, our group is interested in cassava roots (Manihot esculenta) detoxification.

On the roles of AA15 lytic polysaccharide monooxygenases derived from the termite Coptotermes gestroi

Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes which catalyze the oxidative cleavage of polysaccharides. LPMOs belonging to family 15 in the Auxiliary Activity (AA) class from the Carbohydrate-Active Enzyme database are found widespread across the Tree of Life, including viruses, algae, oomycetes and animals. Recently, two AA15s from the firebrat Thermobia domestica were reported to have oxidative activity, one towards cellulose or chitin and the other towards chitin, signalling that AA15 LPMOs from insects potentially have different biochemical functions. Herein, we report the identification and characterization of two family AA15 members from the lower termite Coptotermes gestroi. Addition of Cu(II) to CgAA15a or CgAA15b had a thermostabilizing effect on both. Using ascorbate and O₂ as co-substrates, CgAA15a and CgAA15b were able to oxidize chitin, but showed no activity on celluloses, xylan, xyloglucan and starch. Structural models indicate that the LPMOs from C. gestroi (CgAA15a/CgAA15b) have a similar fold but exhibit key differences in the catalytic site residues when compared to the cellulose/chitin-active LPMO from T. domestica (TdAA15a), especially the presence of a non-coordinating phenylalanine nearby the Cu ion in CgAA15a/b, which appears as a tyrosine in the active site of TdAA15a. Despite the overall similarity in protein folds, however, mutation of the active site phenylalanine in CgAA15a to a tyrosine did not expanded the enzymatic specificity from chitin to cellulose. Our data show that CgAA15a/b enzymes are likely not involved in lignocellulose digestion but might play a role in termite developmental processes as well as on chitin and nitrogen metabolisms.