Diet is the primary determinant of bacterial community structure in the guts of higher termites

Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification

The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont.

Elucidating the structure, and composition of bacterial symbionts in the gut regions of wood-feeding termite, Coptotermes formosanus and their functional profile towards lignocellulolytic systems

The wood-feeding termite, Coptotermes formosanus, presents an efficient lignocellulolytic system, offering a distinctive model for the exploration of host-microbial symbiosis towards lignocellulose degradation. Despite decades of investigation, understanding the diversity, community structure, and functional profiles of bacterial symbionts within specific gut regions, particularly the foregut and midgut of C. formosanus, remains largely elusive. In light of this knowledge gap, our efforts focused on elucidating the diversity, community composition and functions of symbiotic bacteria inhabiting the foregut, midgut, and hindgut of C. formosanus via metagenomics. The termite harbored a diverse community of bacterial symbionts encompassing 352 genera and 26 known phyla, exhibiting an uneven distribution across gut regions. Notably, the hindgut displayed a higher relative abundance of phyla such as Bacteroidetes (56.9%) and Spirochetes (23.3%). In contrast, the foregut and midgut were predominantly occupied by Proteobacteria (28.9%) and Firmicutes (21.2%) after Bacteroidetes. The foregut harbored unique phyla like Candidate phylum_TM6 and Armatimonadetes. At the family level, Porphyromonadaceae (28.1, 40.6, and 53.5% abundance in foregut, midgut, and hindgut, respectively) and Spirochaetaceae (foregut = 9%, midgut = 16%, hindgut = 21.6%) emerged as dominant families in the termite's gut regions. Enriched operational taxonomic units (OTUs) were most abundant in the foregut (28), followed by the hindgut (14), while the midgut exhibited enrichment of only two OTUs. Furthermore, the functional analyses revealed distinct influences of bacterial symbionts on various metabolic pathways, particularly carbohydrate and energy metabolisms of the host. Overall, these results underscore significant variations in the structure of the bacterial community among different gut regions of C. formosanus, suggesting unique functional roles of specific bacteria, thereby inspiring further investigations to resolve the crosstalk between host and microbiomes in individual gut-regions of the termite.

Gut Microbiota Affects Host Fitness of Fall Armyworm Feeding on Different Food Types

The fall armyworm (FAW), Spodoptera frugiperda, seriously threatens food and cash crops. Maize, wheat, and even rice damage by FAWs have been reported in many areas of China. It is urgent to clarify the mechanism which FAWs adapt to different feeding hosts and develop effective control technologies. Two-sex life tables and 16s rDNA sequencing were used to determine the host fitness and gut microbial diversity of FAWs when fed four different food types. Considering the life history parameters, pupa weight, and nutrient utilization indexes, the host fitness of FAWs when fed different food types changed in descending order as follows: artificial diet, maize, wheat, and rice. The gut microbial composition and the diversity of FAWs when fed different food types were significantly different, and those changes were driven by low-abundant bacteria. The gut microbes of FAWs that were fed with maize had the highest diversity. The functions of the gut microbes with significant abundance differences were enriched in nutrient and vitamin metabolism and other pathways that were closely related to host adaptation. Furthermore, we identified five genera (Acinetobacter, Variovorax, Pseudomonas, Bacillus, and Serratia) and one genus (Rahnella) that were positively and negatively correlated with the host fitness, respectively. This study revealed the possible role of gut microbes in the host adaptation of FAWs.

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.

Comparison of the Intestinal Bacterial Communities between Captive and Semi-Free-Range Red-Crowned Cranes (Grus japonensis) before Reintroduction in Zhalong National Nature Reserve, China

The wild populations of red-crowned cranes (Grus japonensis) in west China are gradually decreasing, necessitating the optimization of reintroduction measures. This study used 16S rRNA high-throughput sequencing technology to compare the gut microbiota communities of cranes living in two modes (captive and semi-free-range) before their reintroduction in Zhalong National Nature Reserve, Heilongjiang Province, China. The results showed that Proteobacteria (74.39%) and Firmicutes (25.29%) were the dominant gut bacterial phyla inhabiting these cranes. Significant differences were found in the gut microbiota community composition between semi-free-range and captive cranes (p < 0.01). Psychrobacter, Sporosarcina, and Lactococcus were significantly enriched in captive cranes (p < 0.05), while Pseudomonadaceae_Pseudomonas, Pantoea, Lysobacter, and Enterobacteriaceae_Pseudomonas were more abundant in semi-free-range cranes (p < 0.05). The functions and community structure of gut microbiota were affected by feeding patterns (p < 0.05). The metabolic pathways of ethylbenzene degradation, PPAR signaling pathway, betalain biosynthesis, systemic lupus erythematosus, and shigellosis were up-regulated in semi-free-range cranes (p < 0.05).

The Correlation between the Gut Microbiota of Endoclita signifer (Lepidoptera, Hepialidae) Larvae and Their Host Preferences

Insects' gut microbiota plays a crucial role in their host selection, adaptation, and plasticity. This study explored the impact of gut bacteria on the adaptation of host selection under different stresses (diverse feeding preferences and no feeding preferences). The seventh instar E. signifer larvae were artificially transferred from the most-selected host E. grandis × E. urophylla (Es) to more preferred hosts, M. apelta (Ma), as well as the non-preferred host, B. papyrifera (Bp). We then obtained the larval gut of three different feeding preference hosts. The gut bacterial DNA was sequenced and analyzed based on 16S rRNA. There were significant differences in the composition of dominant gut bacteria between Es with Ma and Bp, but without significant differences between Ma and Bp. In the process, Burkholderia and Microbacillus with degrading pesticides had significant changes, and Enterococcus with insect gut probiotics also had significant changes. The presence of enterococcus may be one of the main causes of intestinal microbiota changes before and after host transfer. Notably, when the feeding of E. signifer changes, the complex connections that exist between gut bacteria also change. Additionally, there was a negative correlation between the feeding preferences of E. signifer and the metabolic functions of their gut bacteria. This study provided a theoretical basis for the prediction and use of gut bacteria to interfere with the feeding of E. signifer.

Convergence of gut microbiota in myrmecophagous amphibians

The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.

Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade

The Clostridia is a dominant bacterial class in the guts of various animals and are considered to nutritionally contribute to the animal host. Here, we discovered clostridial endosymbionts of cellulolytic protists in termite guts, which have never been reported with evidence. We obtained (near-)complete genome sequences of three endosymbiotic Clostridia, each associated with a different parabasalid protist species with various infection rates: Trichonympha agilis, Pseudotrichonympha grassii, and Devescovina sp. All these protists are previously known to harbor permanently-associated, mutualistic Endomicrobia or Bacteroidales that supplement nitrogenous compounds. The genomes of the endosymbiotic Clostridia were small in size (1.0-1.3 Mbp) and exhibited signatures of an obligately-intracellular parasite, such as an extremely limited capability to synthesize amino acids, cofactors, and nucleotides and a disrupted glycolytic pathway with no known net ATP-generating system. Instead, the genomes encoded ATP/ADP translocase and, interestingly, regulatory proteins that are unique to eukaryotes in general and are possibly used to interfere with host cellular processes. These three genomes formed a clade with metagenome-assembled genomes (MAGs) derived from the guts of other animals, including human and ruminants, and the MAGs shared the characteristics of parasites. Gene flux analysis suggested that the acquisition of the ATP/ADP translocase gene in a common ancestor was probably key to the emergence of this parasitic clade. Taken together, we provide novel insights into the multilayered symbiotic system in the termite gut by adding the presence of parasitism and present an example of the emergence of putative energy parasites from a dominant gut bacterial clade.

Gut microbial diversity and function analysis of the final-instar larvae of Protohermes xanthodes (Megaloptera: Corydalidae)

Protohermes xanthodes (Megaloptera, Corydalidae, Protohermes), widespread species in China, is an important insects treated as food and medicine for aquaculture. In this study, the gut microbiota was investigated by 16S rRNA microbial profiling. A total of 600 Amplicon Sequence Variants (ASV) were identified, Proteobacteria and Firmicutes were the main dominant phyla, and 27 genera ran through the entire digestive tract, mainly Hafnia-Obesumbacterium (Proteobacteria), Lactobacillus and Lactococcus (Firmicutes). The PICRUSt2 functional prediction of gut microbiota showed that the foregut abundant pathways related to metabolism, environmental information processing, and genetic information processing. while the midgut had the most abundant metabolic and environmental information processing pathways, including the prominent phosphotransferase system (PTS), propionate metabolism, and β-lactam resistance. The hindgut had the weakest metabolic function, but its genetic information processing was more abundant than the foregut and midgut. Additionally, 26 strains of bacteria were isolated from the midgut microorganisms, with Firmicutes being the dominant bacteria, and some of the purified bacteria had potential probiotic and anti-pathogen functions. These findings suggest that there are differences in the microorganisms of the different gut floras of the larvae, and each flora has specific metabolic functions. This research could be used to further understand the function of gut microorganisms, explore the co-evolution of P. xanthodes and gut microorganisms, and promote healthy breeding based on gut microorganisms.

Evidence of cospeciation between termites and their gut bacteria on a geological time scale

Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one Cryptocercus cockroach, we show that bacteria endemic to termite guts are mostly transferred vertically. We identified 18 lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for 16 bacterial lineages were within the range of those estimated for 15 mitochondrial genes, suggesting that horizontal transfers are uncommon and vertical transfers are the dominant transmission route in these lineages. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.

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.

Basic Structures of Gut Bacterial Communities in Eusocial Insects

Gut bacterial communities assist host animals with numerous functions such as food digestion, nutritional provision, or immunity. Some social mammals and insects are unique in that their gut microbial communities are stable among individuals. In this review, we focus on the gut bacterial communities of eusocial insects, including bees, ants, and termites, to provide an overview of their community structures and to gain insights into any general aspects of their structural basis. Pseudomonadota and Bacillota are prevalent bacterial phyla commonly detected in those three insect groups, but their compositions are distinct at lower taxonomic levels. Eusocial insects harbor unique gut bacterial communities that are shared within host species, while their stability varies depending on host physiology and ecology. Species with narrow dietary habits, such as eusocial bees, harbor highly stable and intraspecific microbial communities, while generalists, such as most ant species, exhibit relatively diverse community structures. Caste differences could influence the relative abundance of community members without significantly altering the taxonomic composition.

Genome-scale community modeling for deciphering the inter-microbial metabolic interactions in fungus-farming termite gut microbiome

Specialized microbial communities in the fungus-farming termite gut and fungal comb microbiome help maintain host nutrition through interactive biochemical activities of complex carbohydrate degradation. Numerous research studies have been focused on identifying the microbial species in the termite gut and fungal comb microbiota, but the community-wide metabolic interaction patterns remain obscure. The inter-microbial metabolic interactions in the community environment are essential for executing biochemical processes like complex carbohydrate degradation and maintaining the host's physicochemical homeostasis. Recent progress in high-throughput sequencing techniques and mathematical modeling provides suitable platforms for constructing multispecies genome-scale community metabolic models that can render sound knowledge about microbial metabolic interaction patterns. Here, we have implemented the genome-scale metabolic modeling strategy to map the relationship between genes, proteins, and reactions of 12 key bacterial species from fungal cultivating termite gut and fungal comb microbiota. The resulting individual genome-scale metabolic models (GEMs) have been analyzed using flux balance analysis (FBA) to optimize the metabolic flux distribution pattern. Further, these individual GEMs have been integrated into genome-scale community metabolic models where a heuristics-based computational procedure has been employed to track the inter-microbial metabolic interactions. Two separate genome-scale community metabolic models were reconstructed for the O. badius gut and fungal comb microbiome. Analysis of the community models showed up to ∼167% increased flux range in lignocellulose degradation, amino acid biosynthesis, and nucleotide metabolism pathways. The inter-microbial metabolic exchange of amino acids, SCFAs, and small sugars was also upregulated in the multispecies community for maximum biomass formation. The flux variability analysis (FVA) has also been performed to calculate the feasible flux range of metabolic reactions. Furthermore, based on the calculated metabolic flux values, newly defined parameters, i.e., pairwise metabolic assistance (PMA) and community metabolic assistance (CMA) showed that the microbial species are getting up to 15% higher metabolic benefits in the multispecies community compared to pairwise growth. Assessment of the inter-microbial metabolic interaction patterns through pairwise growth support index (PGSI) indicated an increased mutualistic interaction in the termite gut environment compared to the fungal comb. Thus, this genome-scale community modeling study provides a systematic methodology to understand the inter-microbial interaction patterns with several newly defined parameters like PMA, CMA, and PGSI. The microbial metabolic assistance and interaction patterns derived from this computational approach will enhance the understanding of combinatorial microbial activities and may help develop effective synergistic microcosms to utilize complex plant polymers.

Succession of the microbiota in the gut of reproductives of Macrotermes subhyalinus (Termitidae) at colony foundation gives insights into symbionts transmission

Termites have co-evolved with a complex gut microbiota consisting mostly of exclusive resident taxa, but key forces sustaining this exclusive partnership are still poorly understood. The potential for primary reproductives to vertically transmit their gut microbiota (mycobiome and bacteriome) to offspring was investigated using colony foundations from field-derived swarming alates of Macrotermes subhyalinus. Metabarcoding based on the fungal internal transcribed spacer (ITS) region and the bacterial 16S rRNA gene was used to characterize the reproductives mycobiome and bacteriome over the colony foundation time. The mycobiome of swarming alates differed from that of workers of Macrotermitinae and changed randomly within and between sampling time points, highlighting no close link with the gut habitat. The fungal ectosymbiont Termitomyces was lost early from the gut of reproductives, confirming the absence of vertical transmission to offspring. Unlike fungi, the bacteriome of alates mirrored that of workers of Macroterminae. Key genera and core OTUs inherited from the mother colony mostly persisted in the gut of reproductive until the emergence of workers, enabling their vertical transmission and explaining why they were found in offspring workers. These findings demonstrate that the parental transmission may greatly contribute to the maintenance of the bacteriome and its co-evolution with termite hosts at short time scales.

Coevolutionary legacies for plant decomposition

Coevolution has driven speciation and evolutionary novelty in functional traits across the Tree of Life. Classic coevolutionary syndromes such as plant-pollinator, plant-herbivore, and host-parasite have focused strongly on the fitness consequences during the lifetime of the interacting partners. Less is known about the consequences of coevolved traits for ecosystem-level processes, in particular their 'afterlife' legacies for litter decomposition, nutrient cycling, and the functional ecology of decomposers. We review the mechanisms by which traits resulting from coevolution between plants and their consumers, microbial symbionts, or humans, and between microbial decomposers and invertebrates, drive plant litter decomposition pathways and rates. This supports the idea that much of current global variation in the decomposition of plant material is a legacy of coevolution.

Gut bacterial communities and their assembly processing in Cnaphalocrocis medinalis from different geographic sources

Introduction

The insect gut harbors numerous microorganisms that may have functions in development and reproduction, digestion, immunity and protection, and detoxification. Recently, the influence factors on gut microbiota were evaluated in the rice leaffolder Cnaphalocrocis medinalis, a widespread insect pest in paddy fields. However, the relationship between gut microbiota composition and geography is poorly understood in C. medinalis.

Methods

To reveal the patterns of C. medinalis gut bacterial communities across geographic sources and the ecological processes driving the patterns, C. medinalis were sampled from six geographic sources in China, Thailand, and Vietnam in 2016, followed by gut bacterial 16S ribosomal RNA gene sequencing.

Results

A total of 22 bacterial phyla, 56 classes, 84 orders, 138 families, 228 genera, and 299 species were generated in C. medinalis from six geographic sources. All alpha diversity indices differed among the samples from different geographic sources. Analysis of similarity (ANOSIM) and permutational multivariate analysis of variance (PERMANOVA) both revealed significant differences in the gut microbiota of C. medinalis from six geographic sources. A total of 94 different taxa were screened as indicators for the gut microbiota of C. medinalis from six geographic sources by linear discriminant analysis effect size (LEfSe). The gene ontology (GO) pathways of the gut microbiota in C. medinalis differed among geographic sources. In total, the bacterial communities within geographic sources were mainly determined by stochastic processes, and those between geographic sources were mainly determined by deterministic processes.

Discussion

This study elucidates that geography plays a crucial role in shaping the gut microbiota of C. medinalis. Thus, it enriches our knowledge of gut bacteria in C. medinalis and sheds light on the mechanisms underlying C. medinalis gut microbial shifts across geography.

Effects of habitat and sampling time on bacterial community composition and diversity in the gut of the female house fly, Musca domestica Linnaeus (Diptera: Muscidae)

Adult house flies feed and breed in a variety of microbe-rich habitats and serve as vectors for human and animal pathogens. To better understand their role in harbouring and disseminating bacteria, we characterized the composition and diversity of bacterial communities in the gut of female house flies collected from three different habitats in Kansas: agricultural (dairy farm), urban (business area dumpsters) and mixed (business located between residential and animal agriculture areas). Bacterial community composition and diversity were influenced more by the house flies' habitat than by sampling time. The most abundant taxa were also highly prevalent in the house flies collected from all three habitats, potentially representing a 'core microbiome' attributable to the fly's trophic and reproductive associations with substrates and food sources comprised of decaying matter and/or animal waste. Bacterial taxa associated with vertebrate guts/faeces and potential pathogens were highly abundant in agricultural fly microbial communities. Interestingly, taxa of potential pathogens were highly abundant in flies from the mixed and urban sites. House flies harboured diverse bacterial communities influenced by the habitat in which they reside, including potential human and animal pathogens, further bolstering their role in the dissemination of pathogens, and indicating their utility for pathogen surveillance.

Food origin influences microbiota and stable isotope enrichment profiles of cold-adapted Collembola (Desoria ruseki)

Collembola are a group of globally distributed microarthropods that can tolerate low temperature and are active in extremely cold environments. While it is well known that animal diets can shape their microbiota, the microbiota of soil animals is not well described, particularly for animals with limited food resources, such as Collembola active in winter at low temperatures. In this study, we explored the effects of three different food sources; corn litter (agriculture grain residuals), Mongolian oak litter (natural plant residuals), and yeast (common food for Collembola culture), on the microbiota of a winter-active Collembola species, Desoria ruseki. We found that microbial diversity and community composition of the Collembola were strongly altered after feeding with different food sources for 30 days. Collembola individuals fed on corn litter harbored the highest bacterial richness and were dominated by a representative of Microbacteriaceae. In contrast, those fed on yeast exhibited the lowest bacterial richness and were primarily colonized by Pseudomonas. The microbial communities associated with the winter-active Collembola differed significantly from those observed in the food. Collembola nutrient turnover also differed when cultured with different food sources, as indicated by the C and N stable isotopic signatures. Our study highlights microbial associations with stable isotopic enrichments of the host. Specifically, the Arthrobacter was positively correlated with δ¹³C enrichment in the host. Representatives of Microbacteriaceae, Micrococcaceae, TM7a, Devosia, and Rathayibacter were positively correlated with δ¹⁵N enrichment of the host. Our study indicates that food sources are major determinants for Collembola microbiota that simultaneously alter consumers' isotopic niches, thereby improving our understanding of the roles played by host-microbiota interactions in sustaining soil biodiversity during the winter.

Exploring the region-wise diversity and functions of symbiotic bacteria in the gut system of wood-feeding termite, Coptotermes formosanus, toward the degradation of cellulose, hemicellulose, and organic dyes

The wood-feeding termite Coptotermes formosanus represents a unique and impressive system for lignocellulose degradation. The highly efficient digestion of lignocellulose is achieved through symbiosis with gut symbionts like bacteria. Despite extensive research during the last three decades, diversity of bacterial symbionts residing in individual gut regions of the termite and their associated functions is still lacking. To this end, cellulose, xylan, and dye-decolorization bacteria residing in foregut, midgut, and hindgut regions of C. formosanus were enlisted by using enrichment and culture-dependent molecular methods. A total of 87 bacterial strains were successfully isolated from different gut regions of C. formosanus which belonged to 27 different species of 10 genera, majorly affiliated with Proteobacteria (80%) and Firmicutes (18.3%). Among the gut regions, 37.9% of the total bacterial isolates were observed in the hindgut that demonstrated predominance of cellulolytic bacteria (47.6%). The majority of the xylanolytic and dye-decolorization bacteria (50%) were obtained from the foregut and midgut, respectively. Actinobacteria represented by Dietza sp. was observed in the hindgut only. Based on species richness, the highest diversity was observed in midgut and hindgut regions each of which harbored seven unique bacterial species. The members of Enterobacter, Klebsiella, and Pseudomonas were common among the gut regions. The lignocellulolytic activities of the selected potential bacteria signpost their assistance to the host for lignocellulose digestion. The overall results indicate that C. formosanus harbors diverse communities of lignocellulolytic bacteria in different regions of the gut system. These observations will significantly advance our understanding of the termite-bacteria symbiosis and their microbial ecology uniquely existed in different gut regions of C. formosanus, which may further shed a light on its potential values at termite-modeled biotechnology.

Comparison of Gut Bacterial Communities of Locusta migratoria manilensis (Meyen) Reared on Different Food Plants

Simple Summary

Although locusts can cause major agricultural damage, they also constitute a valuable food resource. At present, L. migratoria manilensis has been largely domesticated, being considered an edible insect in China. Feeding variety is one of the main characteristics of L. migratoria manilensis. There are apparent differences in the capacity of locusts to adapt to different food plants. To elucidate the effect of different food plants (i.e., goosegrass, maize leaves, soybean leaves, and pakchoi) on the growth and development of L. migratoria manilensis, the gut bacterial community composition of L. migratoria manilensis fifth instars fed on different plants was analyzed by high-throughput sequencing. Gut bacterial communities were affected by food plants and may play an essential role in host adaption. Feeding on different food plants has significant effects on the growth and development of L. migratoria manilensis. The present study establishes a theoretical foundation for studying the interplay between gut bacteria structure and L. migratoria manilensis adaptation.

Abstract

Locusts, in particular Locusta migratoria manilensis (Meyen), have been associated with major damages in agriculture, forestry, and animal husbandry in China. At present, L. migratoria manilensis has been largely domesticated, being considered an edible insect in China. Feeding variety is one of the main characteristics of L. migratoria manilensis. It has been demonstrated that microorganisms inhabiting the insect gut impact nutrition, development, defense, and reproduction of the insect host. The aim of the present study was to search for the adaptation mechanism of L. migratoria manilensis feeding on four different food plants (goosegrass, maize leaves, soybean leaves, and pakchoi) and explore changes in the gut bacterial community structure of the insect at the fifth instar nymph stage. Proteobacteria and Firmicutes were the dominant phyla, whereas Kluyvera, Enterobacter, Pseudocitrobacter, Klebsiella, Cronobacter, Citrobacter, Lactococcus, and Weissella were the dominant genera in the gut of L. migratoria manilensis. Principal component analysis and permutational multivariate analysis of variance (PERMANOVA) revealed significant differences in the gut microbiota structure of L. migratoria manilensis fed on different food plants. Moreover, functional prediction analysis revealed that metabolic and cellular processes were the most enriched categories. Within the category of metabolic processes, the most enriched pathways were carbohydrate transport and metabolism; amino acid transport and metabolism; translation, ribosomal structure, and biogenesis; cell wall/membrane/envelope biogenesis; inorganic ion transport and metabolism; and energy production and conversion. Collectively, the present results revealed that the structure of gut bacterial communities in L. migratoria manilensis fed on different food plants is impacted by food plants, which may play an essential part in the adaptation of the host.

The Role of Feeding Characteristics in Shaping Gut Microbiota Composition and Function of Ensifera (Orthoptera)

Feeding habits were the primary factor affecting the gut bacterial communities in Ensifera. However, the interaction mechanism between the gut microbiota and feeding characteristics is not precisely understood. Here, the gut microbiota of Ensifera with diverse feeding habits was analyzed by shotgun metagenomic sequencing to further clarify the composition and function of the gut microbiota and its relationship with feeding characteristics. Our results indicate that under the influence of feeding habits, the gut microbial communities of Ensifera showed specific characteristics. Firstly, the gut microbial communities of the Ensifera with different feeding habits differed significantly, among which the gut microbial diversity of the herbivorous Mecopoda niponensis was the highest. Secondly, the functional genes related to feeding habits were in high abundance. Thirdly, the specific function of the gut microbial species in the omnivorous Gryllotalpa orientalis showed that the more diverse the feeding behavior of Ensifera, the worse the functional specificity related to the feeding characteristics of its gut microbiota. However, feeding habits were not the only factors affecting the gut microbiota of Ensifera. Some microorganisms' genes, whose functions were unrelated to feeding characteristics but were relevant to energy acquisition and nutrient absorption, were detected in high abundance. Our results were the first to report on the composition and function of the gut microbiota of Ensifera based on shotgun metagenomic sequencing and to explore the potential mechanism of the gut microbiota's association with diverse feeding habits.

A comprehensive comparison of fecal microbiota in three ecological bird groups of raptors, waders, and waterfowl

Gut microbiota plays a vital role in maintaining the health and immunity of wild birds. However, less is known about the comparison of fecal microbiota between different ecological groups of wild birds, particularly in the Yellow River National Wetland in Baotou, China, an important transit point for birds migrating all over the East Asia-Australian and Central Asian flyways. In this study, we characterized the fecal microbiota and potential microbial function in nine bird species of raptors, waders, and waterfowl using 16S rRNA gene amplicon sequencing to reveal the microbiota differences and interaction patterns. The results indicated that there was no significant difference in α-diversity, but a significant difference in β-diversity between the three groups of birds. The fecal bacterial microbiota was dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes in all groups of birds. Furthermore, we identified five bacterial genera that were significantly higher in raptors, five genera that were significantly higher in waders, and two genera that were more abundant in waterfowl. The bacterial co-occurrence network results revealed 15 and 26 key genera in raptors and waterfowls, respectively. The microbial network in waterfowl exhibited a stronger correlation pattern than that in raptors. PICRUSt2 predictions indicated that fecal bacterial function was significantly enriched in the antibiotic biosynthesis pathway in all three groups. Metabolic pathways related to cell motility (bacterial chemotaxis and flagellar assembly) were significantly more abundant in raptors than in waders, whereas waders were enriched in lipid metabolism (synthesis and degradation of ketone bodies and fatty acid biosynthesis). The fecal microbiota in waterfowl harbored more abundant vitamin B6 metabolism, RNA polymerase, and tyrosine and tryptophan biosynthesis. This comparative study revealed the microbial community structure, microbial co-occurrence patterns, and potential functions, providing a better understanding of the ecology and conservation of wild birds. Future studies may focus on unraveling metagenomic functions and dynamics along with the migration routine or different seasons by metagenomics or metatranscriptomics.

Investigation of Gut Bacterial Communities of Asian Citrus Psyllid (Diaphorina citri) Reared on Different Host Plants

Simple Summary

Diaphorina citri is a crucial natural vector of the Huanglongbing pathogen, which has devastated the citrus industry. The host plant is a critical factor that affects insect biology and its symbiont abundance. However, little is known about how host plants affect the bacterial community located in D. citri. In this work, the guts of five different host-plant-feeding populations (i.e., Citrus reticulata cv. Shatangju, Citrus poonensis cv. Ponkan, Murraya paniculata (orange jasmine), Citrus limon (lemon), and Citrus sinensis (navel orange)) were analyzed for bacterial communities by next-generation sequencing. The dominant phylum was Proteobacteria. The most common and abundant bacterial genera in D. citri were Wolbachia, Escherichia-Shigella, and Candidatus Profftella, but their relative abundance varied among the different host plant groups. There were obvious differences in the gut microbiota among the different hosts, and the gut microbe diversity was the highest in the ponkan-feeding population, while the lowest was in the Shatangju-feeding population. Overall, our findings indicate that the host plant can significantly affect the gut microbial community of D. citri. This result can provide new insights into the co-adaptation of D. citri and its symbionts.

Abstract

Diaphorina citri Kuwayama (Hemiptera: Liviidae) can cause severe damage to citrus plants, as it transmits Candidatus Liberibacter spp., a causative agent of Huanglongbing disease. Symbiotic bacteria play vital roles in the ecology and biology of herbivore hosts, thereby affecting host growth and adaptation. In our research, the effects of Rutaceous plants (i.e., Citrus reticulata cv. Shatangju, Citrus poonensis cv. Ponkan, Murraya paniculata (orange jasmine), Citrus limon (lemon), and Citrus sinensis (navel orange)) on the gut microbiota (GM) and microbial diversity of D. citri adults were investigated by 16S rRNA high-throughput sequencing. It was found that Proteobacteria dominated the GM communities. The gut microbe diversity was the highest in the ponkan-feeding population, and the lowest in the Shatangju-feeding population. The NMDS analysis revealed that there were obvious differences in the GM communities among the different hosts. PICRUSt function prediction indicated significant differences in host function, and those pathways were crucial for maintaining population reproduction, growth, development, and adaptation to environmental stress in D. citri. Our study sheds new light on the interactions between symbionts, herbivores, and host plants and expands our knowledge on host adaptation related to GM in D. citri.

In Vitro Studies Reveal that Pseudomonas, from Odontotermes obesus Colonies, can Function as a Defensive Mutualist as it Prevents the Weedy Fungus While Keeping the Crop Fungus Unaffected

Insects that farm monocultures of fungi are canonical examples of nutritional symbiosis as well as independent evolution of agriculture in non-human animals. But just like in human agriculture, these fungal crops face constant threat of invasion by weeds which, if unchecked, take over the crop fungus. In fungus-growing termites, the crop fungus (Termitomyces) faces such challenges from the weedy fungus Pseudoxylaria. The mechanism by which Pseudoxylaria is suppressed is not known. However, evidence suggests that some bacterial secondary symbionts can serve as defensive mutualists by preventing the growth of Pseudoxylaria. However, such secondary symbionts must possess the dual, yet contrasting, capabilities of suppressing the weedy fungus while keeping the growth of the crop fungus unaffected. This study describes the isolation, identification, and culture-dependent estimation of the roles of several such putative defensive mutualists from the colonies of the wide-spread fungus-growing termite from India, Odontotermes obesus. From the 38 bacterial cultures tested, a strain of Pseudomonas showed significantly greater suppression of the weedy fungus than the crop fungus. Moreover, a 16S rRNA pan-microbiome survey, using the Nanopore platform, revealed Pseudomonas to be a part of the core microbiota of O. obesus. A meta-analysis of microbiota composition across different species of Odontotermes also confirms the widespread prevalence of Pseudomonas within this termite. These lines of evidence indicate that Pseudomonas could be playing the role of defensive mutualist within Odontotermes.

Mining the diversity and functional profile of bacterial symbionts from the larvae of Chironomus circumdatus (bloodworms)

Chironomids are the most abundant aquatic insects in freshwater habitats that can survive in extreme conditions. In this study, as the microbiome provides extended genotype to the host to perform various functions, we explored the microbiota of the Chironomus circumdatus larvae to find out the putative role played by the symbiotic bacteria for the host. The metabarcoding analyses of the larvae revealed that the insect harbors 1771 phylotypes. Out of the various microbial communities found, the majority corresponded to the phyla Proteobacteria (52.59%) and Actinobacteria (20.56%), respectively. The midges also harbored Klebsiella (2.57%), Enterobacter (1.32%), Bacillus (2.29%), and Acinetobacter (2.13%) genera that are involved in detoxification of xenobiotics present in the water. The presence of radiation-resistant genera like Deinococcus, including bacterial species like radiodurans, a highly radiation-resistant bacterium, indicates its potential to support the host's ability to sustain in adverse environments. The functional profiling of the bacteria showed the relative abundance of many enzyme groups, such as transferases (40.62%), oxidoreductases (23.49%), and hydrolases (3.77%). The results indicate that the larvae harbor a considerable variety of bacteria that help the host adapt and survive in the polluted waters. The present study provides thorough insights into the microbiome of the C. circumdatus larvae that can be exploited for the bioremediation of certain pollutants through biomimetic strategies. It also gives us a wake-up call to take a good look at the guts of these disease-carrying insects' inabilities to spread deadly human diseases.

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.

Effects of Host Plants on Bacterial Community Structure in Larvae Midgut of Spodoptera frugiperda

Simple Summary

The gut microbiota plays an important role in insect physiology and behavior. The interaction among the different structures of gut bacterial community in the fall armyworm (FAW), Spodoptera frugiperda, and different host plants, and whether these different gut bacteria are responsible for the rapid spread of FAW to a variety of host plants after invasion are largely unexplored. In the present paper, we used a culture-independent approach targeting the bacterial 16S rRNA gene of gut bacteria of the 5th instar larvae of FAW fed on four different host plants. It aimed to analyze the effects of host plants on gut bacteria abundance, community structure and metabolic function. We found that host plants exerted considerable effects on the structure and composition of the gut bacteria in FAW and the differences among the four groups identified were significant. They were related to the detoxification and adaptation of FAW to toxic secondary metabolites of the host plant. These differences enabled the gut microbiome to perform different functions. This study lays a foundation for further studies on the function of intestinal bacteria in FAW and the adaptive mechanism to the host.

Abstract

The fall armyworm (FAW), Spodoptera frugiperda, is one of the most important invasive species and causes great damage to various host crops in China. In this study, the diversity and function of gut bacteria in the 5th instar larvae of FAW fed on maize, wheat, potato and tobacco leaves were analyzed through 16S rRNA sequencing. A total of 1324.25 ± 199.73, 1313.5 ± 74.87, 1873.00 ± 190.66 and 1435.25 ± 139.87 operational taxonomic units (OTUs) from the gut of FAW fed on these four different host plants were detected, respectively. Firmicutes, Proteobacteria and Bacteroidetes were the most abundant bacterial phyla. Beta diversity analysis showed that the gut bacterial community structure of larvae fed on different host plants was significantly differentiated. At the genus level, the abundance of Enterococcus in larvae fed on wheat was significantly lower than those fed on the other three host plants. Enterobacter and ZOR0006 were dominant in FAW fed on tobacco leaves, and in low abundance in larvae fed on wheat. Interestingly, when fed on Solanaceae (tobacco and potato) leaves which contained relative higher levels of toxic secondary metabolites than Gramineae (wheat and maize), the genera Enterococcus, Enterobacter and Acinetobacter were significantly enriched. The results indicated that gut bacteria were related to the detoxification and adaptation of toxic secondary metabolites of host plants in FAW. Further analysis showed that replication, repair and nucleotide metabolism functions were enriched in the gut bacteria of larvae fed on tobacco and potato. In conclusion, the gut bacterial diversity and community composition in FAW larvae fed on different host plants showed significant differences, and the insect is likely to regulate their gut bacteria for adaptation to different host plants.

The Biodegradation of Soil Organic Matter in Soil-Dwelling Humivorous Fauna

Soil organic matter contains more carbon than global vegetation and the atmosphere combined. Gaining access to this source of organic carbon is challenging and requires at least partial removal of polyphenolic and/or soil mineral protections, followed by subsequent enzymatic or chemical cleavage of diverse plant polysaccharides. Soil-feeding animals make significant contributions to the recycling of terrestrial organic matter. Some humivorous earthworms, beetles, and termites, among others, have evolved the ability to mineralize recalcitrant soil organic matter, thereby leading to their tremendous ecological success in the (sub)tropical areas. This ability largely relies on their symbiotic associations with a diverse community of gut microbes. Recent integrative omics studies, including genomics, metagenomics, and proteomics, provide deeper insights into the functions of gut symbionts. In reviewing this literature, we emphasized that understanding how these soil-feeding fauna catabolize soil organic substrates not only reveals the key microbes in the intestinal processes but also uncovers the potential novel enzymes with considerable biotechnological interests.

Evidence of sodium limitation in ants and termites in a Neotropical savanna

Nutritional ecology of ropical ecosystems like Neotropical savannas, which are of high conservation concern, is understudied. Sodium is essential for heterotrophs but availability often falls short relative to plant consumer requirements. Savanna plant consumers like ants and termites should be sodium-limited due to high temperatures, nutrient-poor soils, and lack of oceanic sodium deposition. We tested the hypothesis that Neotropical savanna ants and termites are sodium-limited. Termites were tested by supplementing 0.25 m2 plots with H2O (control), 0.1%, 0.5%, or 1.0% NaCl and measuring termite presence and artificial substrate mass loss after 1 week. Ants were tested by collecting ants that recruited to H2O (control), 0.1%, 0.5%, and 1.0% NaCl and 1.0%, 10%, and 20% sugar baits on paired diurnal–nocturnal transects. Termites were 16 times more likely to occur on 1% NaCl than H2O plots and wood-feeding termites were most frequent. However, the decomposition rate did not differ among treatments. Ant bait use increased with increasing NaCl concentration and 1% NaCl usage was similar to sugar bait usage. Ants were 3.7 times more active nocturnally than diurnally, but contrary to predictions bait type (water, sugar or NaCl) usage did not differ between day and night. Together, these results provide strong evidence of sodium limitation in Neotropical savannas.

Species- and Caste-Specific Gut Metabolomes in Fungus-Farming Termites

Fungus-farming termites host gut microbial communities that contribute to the pre-digestion of plant biomass for manuring the fungal mutualist, and potentially to the production of defensive compounds that suppress antagonists. Termite colonies are characterized by complex division of labor and differences in diet between termite size (minor and major) and morphological (worker and soldier) castes, and this extends to the composition of their gut microbial communities. We hypothesized that gut metabolomes should mirror these differences and tested this through untargeted LC-MS/MS analyses of three South African species of fungus-farming termites. We found distinct metabolomes between species and across castes, especially between soldiers and workers. Primary metabolites dominate the metabolomes and the high number of overlapping features with the mutualistic fungus and plant material show distinct impacts of diet and the environment. The identification of a few bioactive compounds of likely microbial origin underlines the potential for compound discovery among the many unannotated features. Our untargeted approach provides a first glimpse into the complex gut metabolomes and our dereplication suggests the presence of bioactive compounds with potential defensive roles to be targeted in future studies.

Host species identity shapes the diversity and structure of insect microbiota

As for most of the life that inhabits our planet, microorganisms play an essential role in insect nutrition, reproduction, defence, and support their host in many other functions. More recently, we assisted to an exponential growth of studies describing the taxonomical composition of bacterial communities across insects' phylogeny. However, there is still an outstanding question that needs to be answered: Which factors contribute most to shape insects' microbiomes? This study tries to find an answer to this question by taking advantage of publicly available sequencing data and reanalysing over 4000 samples of insect-associated bacterial communities under a common framework. Results suggest that insect taxonomy has a wider impact on the structure and diversity of their associated microbial communities than the other factors considered (diet, sex, life stage, sample origin and treatment). However, when specifically testing for signatures of codiversification of insect species and their microbiota, analyses found weak support for this, suggesting that while insect species strongly drive the structure and diversity of insect microbiota, the diversification of those microbial communities did not follow their host's phylogeny. Furthermore, a parallel survey of the literature highlights several methodological limitations that need to be considered in the future research endeavours.

Microbial community in human gut: a therapeutic prospect and implication in health and diseases

The interest in the working and functionality of the human gut microbiome has increased drastically over the years. Though the existence of gut microbes has long been speculated for long over the last few decades, a lot of research has sprung up in studying and understanding the role of gut microbes in the human digestive tract. The microbes present in the gut are highly instrumental in maintaining the metabolism in the body. Further research is going on in this field to understand how gut microbes can be employed as potential sources of novel therapeutics; moreover, probiotics have also elucidated their significant place in this direction. As regards the clinical perspective, microbes can be engineered to afford defence mechanisms while interacting with foreign pathogenic bodies. More investigations in this field may assist us to evaluate and understand how these cells communicate with human cells and promote immune interactions. Here we elaborate on the possible implication of human gut microbiota into the immune system as well as explore the probiotics in the various human ailments. Comprehensive information on the human gut microbiome at the same platform may contribute effectively to our understanding of the human microbiome and possible mechanisms of associated human diseases.

Diet-induced microbiome shifts of sympatric overwintering birds

Gut microbiota have a significant impact on host physiology and health, and host genetics and diet are considered as two important factors, but it is difficult to discriminate the influence of each single factor (host or diet) on gut microbiota under natural conditions. Moreover, current studies of avian microbiota mainly focus on domestic or captive birds, and it is still uncertain how host and diet take part in changing avian gut microbiota composition, diversity, and function in the wild. Here, high-throughput sequencing of 16S rRNA was used to identify the gut microbiota communities for sympatric wintering Great Bustards and Common Cranes at different diets. The results showed that 8.87% operational taxonomic units (OTUs) were shared among all sampling birds; in contrast, 39.43% of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways were common among all individuals, indicating the existence of gut microbiota conservatism both in microbiota structure and function. Microbiota abundance and diversity differed between Great Bustards and Common Cranes in a specific wintering site, and microbiota variation was detected for the same host species under two different sites, suggesting that the change of gut microbiota was induced by both host and diet. Furthermore, we found that changes of both microbial communities and functional pathways were larger between hosts than those between diets, which revealed that host might be the dominant factor determining microbiota characteristics and function, while diet further drove the divergence of gut microbiota. Gut microbiota functions appeared to be more conserved than bacterial community structure, indicating that different bacteria may function in a similar way, while microbiota OTU diversity might not be necessarily associated with functional diversity. With diet shifting, gut microbiota changed both in terms of microbial communities and functional pathways for the sympatric birds, which implies that avian habitats and their physiological microbiota would be influenced by different farmland management regimes. KEY POINTS: • Gut microbiota can be shaped by both diets and hosts in sympatric species. • Host was the dominant factor shaping the gut microbiota communities and functional pathways. • Gut microbiota were conservative both in structure and in function, but more conservative in function.

Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals

The previous studies have reported that the mammalian gut microbiota is a physiological consequence; nonetheless, the factors influencing its composition and function remain unclear. In this study, to evaluate the contributions of the host and environment to the gut microbiota, we conducted a sequencing analysis of 16S rDNA and shotgun metagenomic DNA from plateau pikas and yaks, two sympatric herbivorous mammals, and further compared the sequences in summer and winter. The results revealed that both pikas and yaks harboured considerably more distinct communities between summer and winter. We detected the over-representation of Verrucomicrobia and Proteobacteria in pikas, and Archaea and Bacteroidetes in yaks. Firmicutes and Actinobacteria, associated with energy-efficient acquisition, significantly enriched in winter. The diversity of the microbial community was determined by the interactive effects between the host and season. Metagenomic analysis revealed that methane-metabolism-related pathway of yaks was significantly enriched in summer, while some pathogenic pathways were more abundant in pikas. Both pikas and yaks had a higher capacity for lipid degradation in winter. Pika and yak shared more OTUs when food shortage occurred in winter, and this caused a convergence in gut microbial composition and function. From winter to summer, the network module number increased from one to five in pikas, which was different in yaks. Our study demonstrates that the host is a dominant factor in shaping the microbial communities and that seasonality promotes divergence or convergence based on dietary quality across host species identity.

Host Phylogeny and Diet Shape Gut Microbial Communities Within Bamboo-Feeding Insects

The gut microbiome plays an important role in a host’s development and adaption to its dietary niche. In this study, a group of bamboo-feeding insects are used to explore the potential role of the gut microbiota in the convergent adaptation to extreme diet specialization. Specifically, using a 16S rRNA marker and an Illumina sequencing platform, we profiled the microbial communities of 76 gut samples collected from nine bamboo-feeding insects, including both hemimetabolous (Orthoptera and Hemiptera) and holometabolous (Coleoptera and Lepidoptera) species, which are specialized in three distinct dietary niches: bamboo leaf, shoot, and sap. The gut microbiota of these insects were dominated by Proteobacteria, Firmicutes, and Bacteroidetes and were clustered into solid (leaf and shoot) and liquid (sap) dietary niches. The gut bacterial communities of insects feeding on solid diet overlapped significantly, even though these insects belong to phylogenetically distant lineages representing different orders. In addition, the presence of cellulolytic bacterial communities within the gut microbiota allows bamboo-feeding insects to adapt to a highly specialized, fiber-rich diet. Although both phylogeny and diet can impact the structure and composition of gut microbiomes, phylogeny is the primary driving force underlying the convergent adaptation to a highly specialized diet, especially when the related insect species harbor similar gut microbiomes and share the same dietary niche over evolutionary timescales. These combined findings lay the foundation for future research on how convergent feeding strategies impact the interplays between hosts and their gut microbiomes and how the gut microbiota may facilitate convergent evolution in phylogenetically distant species in adaptation to the shared diet.

Characterization and phylogenomic analysis of Breznakiella homolactica gen. nov. sp. nov. indicate that termite gut treponemes evolved from non-acetogenic spirochetes in cockroaches

Spirochetes of the genus Treponema are surprisingly abundant in termite guts, where they play an important role in reductive acetogenesis. Although they occur in all termites investigated, their evolutionary origin is obscure. Here, we isolated the first representative of 'termite gut treponemes' from cockroaches, the closest relatives of termites. Phylogenomic analysis revealed that Breznakiella homolactica gen. nov. sp. nov. represents the most basal lineage of the highly diverse 'termite cluster I', a deep-branching sister group of Treponemataceae (fam. 'Termitinemataceae') that was present already in the cockroach ancestor of termites and subsequently coevolved with its host. Breznakiella homolactica is obligately anaerobic and catalyses the homolactic fermentation of both hexoses and pentoses. Resting cells produced acetate in the presence of oxygen. Genome analysis revealed the presence of pyruvate oxidase and catalase, and a cryptic potential for the formation of acetate, ethanol, formate, CO₂ and H₂ - the fermentation products of termite gut isolates. Genes encoding key enzymes of reductive acetogenesis, however, are absent, confirming the hypothesis that the ancestral metabolism of the cluster was fermentative, and that the capacity for acetogenesis from H₂ plus CO₂ - the most intriguing property among termite gut treponemes - was acquired by lateral gene transfer.

Origin of symbiotic gut spirochetes as key players in the nutrition of termites

Termites harbour symbiotic spirochetes in their hindguts, which have long been considered treponemes, although they represent separate lines of descent from known species of Treponema. 'Termite gut treponemes' have a mutualistic relationship with the host termites with their physiological properties including CO₂ -reductive acetogenesis, from which the resulting acetate fulfils most of the respiratory requirement of the host. Song and co-workers showed that a spirochetal isolate (strain RmG30) from a Madeira cockroach represents the earliest branching lineage of extremely diverse termite (Treponema) cluster I and was a simple homolactic fermenter, suggesting that CO₂ -reductive acetogenesis exhibited by some members of termite cluster I originated via horizontal gene transfer. Phylogenomic and 16S rRNA sequence-based phylogenetic analyses indicated a deeply-branched sister clade containing termite cluster I was distinguishable as a family-level lineage. In this context, a new family, 'Termitinemataceae' has been proposed for this clade. Strain RmG30 has been designated as the type strain of Breznakiella homolactica gen. nov. sp. nov. named after John A. Breznak, an American microbiologist distinguished in termite gut microbiology. The study has posed important questions for the future, including the actual roles of the termite spirochetes in each termite lineage and the evolutionary process of their physiological properties.

Complementary Contribution of Fungi and Bacteria to Lignocellulose Digestion in the Food Stored by a Neotropical Higher Termite

Lignocellulose digestion in termites is achieved through the functional synergy between gut symbionts and host enzymes. However, some species have evolved additional associations with nest microorganisms that collaborate in the decomposition of plant biomass. In a previous study, we determined that plant material packed with feces inside the nests of Cornitermes cumulans (Syntermitinae) harbors a distinct microbial assemblage. These food nodules also showed a high hemicellulolytic activity, possibly acting as an external place for complementary lignocellulose digestion. In this study, we used a combination of ITS sequence analysis, metagenomics, and metatranscriptomics to investigate the presence and differential expression of genes coding for carbohydrate-active enzymes (CAZy) in the food nodules and the gut of workers and soldiers. Our results confirm that food nodules express a distinct set of CAZy genes suggesting that stored plant material is initially decomposed by enzymes that target the lignin and complex polysaccharides from fungi and bacteria before the passage through the gut, where it is further targeted by a complementary set of cellulases, xylanases, and esterases produced by the gut microbiota and the termite host. We also showed that the expression of CAZy transcripts associated to endoglucanases and xylanases was higher in the gut of termites than in the food nodules. An additional finding in this study was the presence of fungi in the termite gut that expressed CAZy genes. This study highlights the importance of externalization of digestion by nest microbes and provides new evidence of complementary digestion in the context of higher termite evolution.

Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits

Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.

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.

Gut Bacterial and Fungal Communities of the Wild and Laboratory-Reared Thitarodes Larvae, Host of the Chinese Medicinal Fungus Ophiocordyceps sinensis on Tibetan Plateau

Simple Summary

The ghost moth, Thitarodes sp., is an obligate host of the most precious fungus Ophiocordyceps sinensis on Tibetan plateau. Artificial rearing of the ghost moth at low-altitude laboratory by mimicking the environment of the wild habitat for the cultivation of the Chinese cordyceps has been realized. However, the high mortality of ghost moth larvae by pathogens, low and slow infection, and mummification rate by O. sinensis still constrain the efficient cultivation of the Chinese cordyceps. Both larval gut microbiota and their exploitation in the Thitarodes artificial rearing system have attracted a renewed interest. In the present study, the gut bacterial and fungal communities of the wild and laboratory-reared populations were characterized using both culture-dependent and -independent approaches. The discovery of apparent microbial community shifts between the wild and laboratory-reared ghost moth larvae, many opportunistic pathogenic bacteria and fungi in the gut of the laboratory-reared ghost moth larvae, and the dominant bacteria enriched in the wild ghost moth provide interesting cues for selecting beneficial probiotic bacteria to improve the effectiveness of Thitarodes rearing system and the cultivation of the Chinese cordyceps.

Abstract

By employing a culture-dependent and -independent 16S rRNA and ITS gene high-throughput sequencing analyses, comprehensive information was obtained on the gut bacterial and fungal communities in the ghost moth larvae of three different geographic locations from high-altitude on Tibet plateau and from low-altitude laboratory. Twenty-six culturable bacterial species belonging to 21 genera and 14 fungal species belonging to 12 genera were identified from six populations by culture-dependent method. Carnobacterium maltaromaticum was the most abundant bacterial species from both the wild and laboratory-reared larvae. The most abundant OTUs in the wild ghost moth populations were Carnobacteriaceae, Enterobacteriaceae for bacteria, and Ascomycota and Basidiomycota for fungi. Larval microbial communities of the wild ghost moth from different geographic locations were not significantly different from each other but significant difference in larval microbial community was detected between the wild and laboratory-reared ghost moth. The larval gut of the wild ghost moth was dominated by the culturable Carnobacterium. However, that of the laboratory-reared ghost moth exhibited significantly abundant Wolbachia, Rhizobium, Serratia, Pseudomonas, and Flavobacterium. Furthermore, the larval gut of the wild ghost moth had a significantly higher abundance of Ophiocordyceps but lower abundance of Candida and Aspergillus than that of the laboratory-reared ghost moth.

Termite evolution: mutualistic associations, key innovations, and the rise of Termitidae

Termites are a clade of eusocial wood-feeding roaches with > 3000 described species. Eusociality emerged ~ 150 million years ago in the ancestor of modern termites, which, since then, have acquired and sometimes lost a series of adaptive traits defining of their evolution. Termites primarily feed on wood, and digest cellulose in association with their obligatory nutritional mutualistic gut microbes. Recent advances in our understanding of termite phylogenetic relationships have served to provide a tentative timeline for the emergence of innovative traits and their consequences on the ecological success of termites. While all "lower" termites rely on cellulolytic protists to digest wood, "higher" termites (Termitidae), which comprise ~ 70% of termite species, do not rely on protists for digestion. The loss of protists in Termitidae was a critical evolutionary step that fostered the emergence of novel traits, resulting in a diversification of morphology, diets, and niches to an extent unattained by "lower" termites. However, the mechanisms that led to the initial loss of protists and the succession of events that took place in the termite gut remain speculative. In this review, we provide an overview of the key innovative traits acquired by termites during their evolution, which ultimately set the stage for the emergence of "higher" termites. We then discuss two hypotheses concerning the loss of protists in Termitidae, either through an externalization of the digestion or a dietary transition. Finally, we argue that many aspects of termite evolution remain speculative, as most termite biological diversity and evolutionary trajectories have yet to be explored.

Effects of Food Changes on Intestinal Bacterial Diversity of Wintering Hooded Cranes (Grus monacha)

Simple Summary

The intestinal microbiota plays a vital role in the health of animals, and food is an important factor that influences the intestinal microbial community. During the winter months, waterbirds require certain foods to supply them with energy through the cold winter. Due to changes in the plant resources available to waterbirds, their intestinal bacteria will vary accordingly. In this study, we analysed the relationship between food composition and intestinal bacteria in hooded cranes (Grus monacha). We found that food resources from similar habitats were more similar, and the corresponding hooded crane intestinal bacteria were also more similar. The results show that the intestinal bacteria of hooded cranes had a certain adaptability to the type of food being consumed. This study contributes novel insights into the diet of hooded cranes in the winter months, allowing for improved protection and management strategies.

Abstract

As food is recognised as an important factor affecting the intestinal microbiota, seasonal changes in diet can influence the community composition. The hooded crane (Grus monacha) is an endangered migratory waterbird species, with some of the population wintering in the sallow lakes in the middle and lower Yangtze River floodplain. Their food resources have changed seasonally, with a reduction resulting from wetland degradation. To cope with seasonal changes in food availability, hooded cranes must constantly adjust their foraging strategies to survive. We studied the effect of changes in diet on the intestinal bacterial diversity of hooded cranes at Shengjin Lake, using faecal microanalysis and high-throughput sequencing. The results show that the main foods of hooded cranes were Polygonum criopolitanum, Oryza sativa, and Carex spp., which were significantly related to the composition of the intestinal bacterial community. In addition, foods available from the similar habitats were more similar, and the corresponding hooded crane intestinal bacteria were also more similar. The relative abundance of Lactobacillus acidipiscis in January and March was significantly higher than in November. Our research shows that the intestinal bacteria of hooded cranes actively adapt to diet changes to overcome the negative impact of the reduction in food resources, which is vital to the survival of hooded cranes.

Symbiont-Mediated Digestion of Plant Biomass in Fungus-Farming Insects

Feeding on living or dead plant material is widespread in insects. Seminal work on termites and aphids has provided profound insights into the critical nutritional role that microbes play in plant-feeding insects. Some ants, beetles, and termites, among others, have evolved the ability to use microbes to gain indirect access to plant substrate through the farming of a fungus on which they feed. Recent genomic studies, including studies of insect hosts and fungal and bacterial symbionts, as well as metagenomics and proteomics, have provided important insights into plant biomass digestion across insect-fungal mutualisms. Not only do advances in understanding of the divergent and complementary functions of complex symbionts reveal the mechanism of how these herbivorous insects catabolize plant biomass, but these symbionts also represent a promising reservoir for novel carbohydrate-active enzyme discovery, which is of considerable biotechnological interest.

Termites Are Associated with External Species-Specific Bacterial Communities

All termites have established a wide range of associations with symbiotic microbes in their guts. Some termite species are also associated with microbes that grow in their nests, but the prevalence of these associations remains largely unknown. Here, we studied the bacterial communities associated with the termites and galleries of three wood-feeding termite species by using 16S rRNA gene amplicon sequencing. We found that the compositions of bacterial communities among termite bodies, termite galleries, and control wood fragments devoid of termite activities differ in a species-specific manner. Termite galleries were enriched in bacterial operational taxonomic units (OTUs) belonging to Rhizobiales and Actinobacteria, which were often shared by several termite species. The abundance of several bacterial OTUs, such as Bacillus, Clostridium, Corynebacterium, and Staphylococcus, was reduced in termite galleries. Our results demonstrate that both termite guts and termite galleries harbor unique bacterial communities.IMPORTANCE As is the case for all ecosystem engineers, termites impact their habitat by their activities, potentially affecting bacterial communities. Here, we studied three wood-feeding termite species and found that they influence the composition of the bacterial communities in their surrounding environment. Termite activities have positive effects on Rhizobiales and Actinobacteria abundance and negative effects on the abundance of several ubiquitous genera, such as Bacillus, Clostridium, Corynebacterium, and Staphylococcus Our results demonstrate that termite galleries harbor unique bacterial communities.

Morphological complexity affects the diversity of marine microbiomes

Large eukaryotes support diverse communities of microbes on their surface-epibiota-that profoundly influence their biology. Alternate factors known to structure complex patterns of microbial diversity-host evolutionary history and ecology, environmental conditions and stochasticity-do not act independently and it is challenging to disentangle their relative effects. Here, we surveyed the epibiota from 38 sympatric seaweed species that span diverse clades and have convergent morphology, which strongly influences seaweed ecology. Host identity explains most of the variation in epibiont communities and deeper host phylogenetic relationships (e.g., genus level) explain a small but significant portion of epibiont community variation. Strikingly, epibiota community composition is significantly influenced by host morphology and epibiota richness increases with morphological complexity of the seaweed host. This effect is robust after controlling for phylogenetic non-independence and is strongest for crustose seaweeds. We experimentally validated the effect of host morphology by quantifying bacterial community assembly on latex sheets cut to resemble three seaweed morphologies. The patterns match those observed in our field survey. Thus, biodiversity increases with habitat complexity in host-associated microbial communities, mirroring patterns observed in animal communities. We suggest that host morphology and structural complexity are underexplored mechanisms structuring microbial communities.

The effects of taxonomy, diet, and ecology on the microbiota of riverine macroinvertebrates

Freshwater macroinvertebrates play key ecological roles in riverine food webs, such as the transfer of nutrients to consumers and decomposition of organic matter. Although local habitat quality drives macroinvertebrate diversity and abundance, little is known about their microbiota. In most animals, the microbiota provides benefits, such as increasing the rate at which nutrients are metabolized, facilitating immune system development, and defending against pathogenic attack. Our objectives were to identify the bacteria within aquatic invertebrates and determine whether their composition varied with taxonomy, habitat, diet, and time of sample collection. In 2016 and 2017, we collected 264 aquatic invertebrates from the mainstem Saint John (Wolastoq) River in New Brunswick, Canada, representing 15 orders. We then amplified the V3-V4 hypervariable region of the 16S rRNA gene within each individual, which revealed nearly 20,000 bacterial operational taxonomic units (OTUs). The microbiota across all aquatic invertebrates were dominated by Proteobacteria (69.25% of the total sequence reads), but they differed significantly in beta diversity, both among host invertebrate taxa (genus-, family-, and order-levels) and temporally. In contrast to previous work, we observed no microbiota differences among functional feeding groups or traditional feeding habits, and neither water velocity nor microhabitat type structured microbiota variability. Our findings suggest that host invertebrate taxonomy was the most important factor in modulating the composition of the microbiota, likely through a combination of vertical and horizontal bacterial transmission, and evolutionary processes. This is one of the most comprehensive studies of freshwater invertebrate microbiota to date, and it underscores the need for future studies of invertebrate microbiota evolution and linkages to environmental bacteria and physico-chemical conditions.