Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota

A longitudinal field study of commercial honey bees shows that non-native probiotics do not rescue antibiotic treatment, and are generally not beneficial

Probiotics are widely used in agriculture including commercial beekeeping, but there is little evidence supporting their effectiveness. Antibiotic treatments can greatly distort the gut microbiome, reducing its protective abilities and facilitating the growth of antibiotic resistant pathogens. Commercial beekeepers regularly apply antibiotics to combat bacterial infections, often followed by an application of non-native probiotics advertised to ease the impact of antibiotic-induced gut dysbiosis. We tested whether probiotics affect the gut microbiome or disease prevalence, or rescue the negative effects of antibiotic induced gut dysbiosis. We found no difference in the gut microbiome or disease markers by probiotic application or antibiotic recovery associated with probiotic treatment. A colony-level application of the antibiotics oxytetracycline and tylosin produced an immediate decrease in gut microbiome size, and over the longer-term, very different and persistent dysbiotic effects on the composition and membership of the hindgut microbiome. Our results demonstrate the lack of probiotic effect or antibiotic rescue, detail the duration and character of dysbiotic states resulting from different antibiotics, and highlight the importance of the gut microbiome for honeybee health.

Gut immune responses and evolution of the gut microbiome-a hypothesis

The gut microbiome is an assemblage of microbes that have profound effects on their hosts. The composition of the microbiome is affected by bottom-up, among-taxa interactions and by top-down, host effects, which includes the host immune response. While the high-level composition of the microbiome is generally stable over time, component strains and genotypes will constantly be evolving, with both bottom-up and top-down effects acting as selection pressures, driving microbial evolution. Secretory IgA is a major feature of the gut's adaptive immune response, and a substantial proportion of gut bacteria are coated with IgA, though the effect of this on bacteria is unclear. Here we hypothesize that IgA binding to gut bacteria is a selection pressure that will drive the evolution of IgA-bound bacteria, so that they will have a different evolutionary trajectory than those bacteria not bound by IgA. We know very little about the microbiome of wild animals and even less about their gut immune responses, but it must be a priority to investigate this hypothesis to understand if and how host immune responses contribute to microbiome evolution.

Bacterial-fungal interactions promote parallel evolution of global transcriptional regulators in a widespread Staphylococcus species

Experimental studies of microbial evolution have largely focused on monocultures of model organisms, but most microbes live in communities where interactions with other species may impact rates and modes of evolution. Using the cheese rind model microbial community, we determined how species interactions shape the evolution of the widespread food- and animal-associated bacterium Staphylococcus xylosus. We evolved S. xylosus for 450 generations alone or in co-culture with one of three microbes: the yeast Debaryomyces hansenii, the bacterium Brevibacterium aurantiacum, and the mold Penicillium solitum. We used the frequency of colony morphology mutants (pigment and colony texture phenotypes) and whole-genome sequencing of isolates to quantify phenotypic and genomic evolution. The yeast D. hansenii strongly promoted diversification of S. xylosus. By the end of the experiment, all populations co-cultured with the yeast were dominated by pigment and colony morphology mutant phenotypes. Populations of S. xylosus grown alone, with B. aurantiacum, or with P. solitum did not evolve novel phenotypic diversity. Whole-genome sequencing of individual mutant isolates across all four treatments identified numerous unique mutations in the operons for the SigB, Agr, and WalRK global regulators, but only in the D. hansenii treatment. Phenotyping and RNA-seq experiments highlighted altered pigment and biofilm production, spreading, stress tolerance, and metabolism of S. xylosus mutants. Fitness experiments revealed antagonistic pleiotropy, where beneficial mutations that evolved in the presence of the yeast had strong negative fitness effects in other biotic environments. This work demonstrates that bacterial-fungal interactions can have long-term evolutionary consequences within multispecies microbiomes by facilitating the evolution of strain diversity.

Characterization of the salivary microbiome before and after antibiotic therapy via separation technique

In the present research, the MALDI-TOF MS technique was applied as a tool to rapidly identify the salivary microbiome. In this fact, it has been monitored the changes occurred in molecular profiles under different antibiotic therapy. Significant changes in the composition of the salivary microbiota were noticed not only in relation to the non antibiotic (non-AT) and antibiotic treatment (AT) groups, but also to the used media, the antibiotic therapy and co-existed microbiota. Each antibiotic generates specific changes in molecular profiles. The highest number of bacterial species was isolated in the universal culture medium (72%) followed by the selective medium (48% and 38%). In the case of non-AT patients, the prevalence of Streptococcus salivarius (25%), Streptococcus vestibularis (19%), Streptococcus oralis (13%), and Staphylococcus aureus (6%) was identified while in the case of AT, Streptococcus salivarius (11%), Streptococcus parasanguinis (11%), Staphylococcus epidermidis (12%), Enterococcus faecalis (9%), Staphylococcus hominis (8%), and Candida albicans (6%) were identified. Notable to specified that the Candida albicans was noticed only in AT samples, indicating a negative impact on the antibiotic therapy. The accuracy of the MALDI-TOF MS technique was performed by the 16S rRNA gene sequencing analysis-as a reference method. Conclusively, such an approach highlighted in the present study can help in developing the methods enabling a faster diagnosis of disease changes at the cellular level before clinical changes occur. Once the MALDI tool allows for the distinguishing of the microbiota of non-AT and AT, it may enable to monitor the diseases treatment and develop a treatment regimen for individual patients in relation to each antibiotic. KEY POINTS: The salivary microbiota of antibiotic-treated patients was more bacteria variety MALDI-TOF MS is a promising tool for recording of reproducible molecular profiles Our data can allow to monitor the treatment of bacterial diseases for patients.

Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content

The animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.

Developing Strategies to Help Bee Colony Resilience in Changing Environments

Climate change, loss of plant biodiversity, burdens caused by new pathogens, predators, and toxins due to human disturbance and activity are significant causes of the loss of bee colonies and wild bees. The aim of this review is to highlight some possible strategies that could help develop bee resilience in facing their changing environments. Scientists underline the importance of the links between nutrition, microbiota, and immune and neuroendocrine stress resistance of bees. Nutrition with special care for plant-derived molecules may play a major role in bee colony health. Studies have highlighted the importance of pollen, essential oils, plant resins, and leaves or fungi as sources of fundamental nutrients for the development and longevity of a honeybee colony. The microbiota is also considered as a key factor in bee physiology and a cornerstone between nutrition, metabolism, growth, health, and pathogen resistance. Another stressor is the varroa mite parasite. This parasite is a major concern for beekeepers and needs specific strategies to reduce its severe impact on honeybees. Here we discuss how helping bees to thrive, especially through changing environments, is of great concern for beekeepers and scientists.

Experimental inheritance of antibiotic acquired dysbiosis affects host phenotypes across generations

Microbiomes can enhance the health, fitness and even evolutionary potential of their hosts. Many organisms propagate favorable microbiomes fully or partially via vertical transmission. In the long term, such co-propagation can lead to the evolution of specialized microbiomes and functional interdependencies with the host. However, microbiomes are vulnerable to environmental stressors, particularly anthropogenic disturbance such as antibiotics, resulting in dysbiosis. In cases where microbiome transmission occurs, a disrupted microbiome may then become a contagious pathology causing harm to the host across generations. We tested this hypothesis using the specialized socially transmitted gut microbiome of honey bees as a model system. By experimentally passaging tetracycline-treated microbiomes across worker 'generations' we found that an environmentally acquired dysbiotic phenotype is heritable. As expected, the antibiotic treatment disrupted the microbiome, eliminating several common and functionally important taxa and strains. When transmitted, the dysbiotic microbiome harmed the host in subsequent generations. Particularly, naïve bees receiving antibiotic-altered microbiomes died at higher rates when challenged with further antibiotic stress. Bees with inherited dysbiotic microbiomes showed alterations in gene expression linked to metabolism and immunity, among other pathways, suggesting effects on host physiology. These results indicate that there is a possibility that sublethal exposure to chemical stressors, such as antibiotics, may cause long-lasting changes to functional host-microbiome relationships, possibly weakening the host's progeny in the face of future ecological challenges. Future studies under natural conditions would be important to examine the extent to which negative microbiome-mediated phenotypes could indeed be heritable and what role this may play in the ongoing loss of biodiversity.

Comparative genomics of Lactobacillaceae from the gut of honey bees, Apis mellifera, from the Eastern United States

Lactobacillaceae are an important family of lactic acid bacteria that play key roles in the gut microbiome of many animal species. In the honey bee (Apis mellifera) gut microbiome, many species of Lactobacillaceae are found, and there is functionally important strain-level variation in the bacteria. In this study, we completed whole-genome sequencing of 3 unique Lactobacillaceae isolates collected from hives in Virginia, USA. Using 107 genomes of known bee-associated Lactobacillaceae and Limosilactobacillus reuteri as an outgroup, the phylogenetics of the 3 isolates was assessed, and these isolates were identified as novel strains of Apilactobacillus kunkeei, Lactobacillus kullabergensis, and Bombilactobacillus mellis. Genome rearrangements, conserved orthologous genes (COG) categories and potential prophage regions were identified across the 3 novel strains. The new A. kunkeei strain was enriched in genes related to replication, recombination and repair, the L. kullabergensis strain was enriched for carbohydrate transport, and the B. mellis strain was enriched in transcription or transcriptional regulation and in some genes with unknown functions. Prophage regions were identified in the A. kunkeei and L. kullabergensis isolates. These new bee-associated strains add to our growing knowledge of the honey bee gut microbiome, and to Lactobacillaceae genomics more broadly.

Contribution of omics to biopreservation: Toward food microbiome engineering

Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.

Phylogenomic analysis and metabolic role reconstruction of mutualistic Rhizobiales hindgut symbionts of Acromyrmex leaf-cutting ants

Rhizobiales are well-known plant-root nitrogen-fixing symbionts, but the functions of insect-associated Rhizobiales are poorly understood. We obtained genomes of three strains associated with Acromyrmex leaf-cutting ants and show that, in spite of being extracellular gut symbionts, they lost all pathways for essential amino acid biosynthesis, making them fully dependent on their hosts. Comparison with 54 Rhizobiales genomes showed that all insect-associated Rhizobiales lost the ability to fix nitrogen and that the Acromyrmex symbionts had exceptionally also lost the urease genes. However, the Acromyrmex strains share biosynthesis pathways for riboflavin vitamin, queuosine and a wide range of antioxidant enzymes likely to be beneficial for the ant fungus-farming symbiosis. We infer that the Rhizobiales symbionts catabolize excess of fungus-garden-derived arginine to urea, supplementing complementary Mollicutes symbionts that turn arginine into ammonia and infer that these combined symbiont activities stabilize the fungus-farming mutualism. Similar to the Mollicutes symbionts, the Rhizobiales species have fully functional CRISPR/Cas and R-M phage defenses, suggesting that these symbionts are important enough for the ant hosts to have precluded the evolution of metabolically cheaper defenseless strains.

Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research

Microbial communities on and within the host contact environmental pollutants, toxic compounds, and other xenobiotic compounds. These communities of bacteria, fungi, viruses, and archaea possess diverse metabolic potential to catabolize compounds and produce new metabolites. Microbes alter chemical disposition thus making the microbiome a natural subject of interest for toxicology. Sequencing and metabolomics technologies permit the study of microbiomes altered by acute or long-term exposure to xenobiotics. These investigations have already contributed to and are helping to re-interpret traditional understandings of toxicology. The purpose of this review is to provide a survey of the current methods used to characterize microbes within the context of toxicology. This will include discussion of commonly used techniques for conducting omic-based experiments, their respective strengths and deficiencies, and how forward-looking techniques may address present shortcomings. Finally, a perspective will be provided regarding common assumptions that currently impede microbiome studies from producing causal explanations of toxicologic mechanisms.

Role of gene regulation and inter species interaction as a key factor in gut microbiota adaptation

Gut microbiota is a class of microbial flora present in various eukaryotic multicellular complex animals such as human beings. Their community's growth and survival are greatly influenced by various factors such as host-pathogen, pathogen-environment and genetic regulation. Modern technologies like metagenomics have particularly extended our capacity to uncover the microbial treasures in challenging conditions like communities surviving at high altitude. Molecular characterizations by newly developed sequencing tools have shown that this complex interaction greatly influences microbial adaptation to the environment. Literature shows that gut microbiota alters the genetic expression and switches to an alternative pathway under the influence of unfavorable conditions. The remarkable adaptability of microbial genetic regulatory networks enables them to survive and expand in tough and energy-limited conditions. Variable prevalence of species in various regions has strengthened this initial evidence. In view of the interconnection of the world in the form of a global village, this phenomenon must be explored more clearly. In this regard, recently there has been significant addition of knowledge to the field of microbial adaptation. This review summarizes and shed some light on mechanisms of microbial adaptation via gene regulation and species interaction in gut microbiota.

Isolation of Hermetia illucens larvae core gut microbiota by two different cultivation strategies

Hermetia illucens larvae (black soldier fly larvae, BSFL) convert efficiently organic waste to high quality biomass. To gain knowledge on the specific functions of gut microbes in this process it is a prerequisite to culture members of the core gut microbiota. Two different cultivation strategies were applied here for this purpose, a dilution-to-extinction cultivation and direct plating using six different media to culture aerobic heterotrophic bacteria. A total of 341 isolates were obtained by the dilution-to-extinction cultivation and 138 isolates by direct plating from guts of BSFL reared on chicken feed. Bacterial isolates were phylogenetically identified at the genus level by 16S rRNA gene sequencing (phylotyping) and differentiated at the strain level by genomic fingerprinting (genotyping). The main proportion of isolates was assigned to Proteobacteria, Firmicutes (Bacilli), and Actinobacteria. Predominant genera discussed in literature as member of a potential BSFL core gut microbiota, Providencia, Proteus, Morganella, Enterococcus, Bacillus, and members of the family Enterobacteriaceae, were isolated. A high intra-phylotype diversity was obtained by genomic fingerprinting which was especially enhanced by the dilution-to-extinction cultivation. This study showed that the application of different cultivation strategies including a dilution-to-extinction cultivation helps to culture a higher diversity of the BSFL gut microbiota and that genomic fingerprinting gives a better picture on the genetic diversity of cultured bacteria which cannot be covered by a 16S rRNA gene sequence based identification alone.

A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications

The production of biochemicals requires the use of microbial strains with efficient substrate conversion and excellent environmental robustness, such as Weizmannia coagulans species. So far, the genomes of 47 strains have been sequenced. Herein, we report a comparative genomic analysis of nine strains on the full repertoire of Carbohydrate-Active enZymes (CAZymes), secretion systems, and resistance mechanisms to environmental challenges. Moreover, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immune system along with CRISPR-associated (Cas) genes, was also analyzed. Overall, this study expands our understanding of the strain's genomic diversity of W. coagulans to fully exploit its potential in biotechnological applications.

Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions

Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of ice-associated prey nearly year-round. SB polar bears showed a higher number of total (940 vs. 742) and unique (387 vs. 189) amplicon sequence variants and higher inter-individual variation compared to EG polar bears. Gut microbiome composition differed significantly between the two subpopulations and among sex/age classes, likely driven by diet variation and ontogenetic shifts in the gut microbiome. Dietary tracer analysis using fatty acid signatures for SB polar bears showed that diet explained more intrapopulation variation in gut microbiome composition and diversity than other tested variables, i.e., sex/age class, body condition, and capture year. Substantial differences in the SB gut microbiome relative to EG polar bears, and associations between SB gut microbiome and diet, suggest that the shifting foraging habits of SB polar bears tied to sea ice loss may be altering their gut microbiome, with potential consequences for nutrition and physiology.

Single-cell genomics for resolution of conserved bacterial genes and mobile genetic elements of the human intestinal microbiota using flow cytometry

As our understanding of the importance of the human microbiota in health and disease grows, so does our need to carefully resolve and delineate its genomic content. 16S rRNA gene-based analyses yield important insights into taxonomic composition, and metagenomics-based approaches reveal the functional potential of microbial communities. However, these methods generally fail to directly link genetic features, including bacterial genes and mobile genetic elements, to each other and to their source bacterial genomes. Further, they are inadequate to capture the microdiversity present within a genus, species, or strain of bacteria within these complex communities. Here, we present a method utilizing fluorescence-activated cell sorting for isolation of single bacterial cells, amplifying their genomes, screening them by 16S rRNA gene analysis, and selecting cells for genomic sequencing. We apply this method to both a cultured laboratory strain of Escherichia coli and human stool samples. Our analyses reveal the capacity of this method to provide nearly complete coverage of bacterial genomes when applied to isolates and partial genomes of bacterial species recovered from complex communities. Additionally, this method permits exploration and comparison of conserved and variable genomic features between individual cells. We generate assemblies of novel genomes within the Ruminococcaceae family and the Holdemanella genus by combining several 16S rRNA gene-matched single cells, and report novel prophages and conjugative transposons for both Bifidobacterium and Ruminococcaceae. Thus, we demonstrate an approach for flow cytometric separation and sequencing of single bacterial cells from the human microbiota, which yields a variety of critical insights into both the functional potential of individual microbes and the variation among those microbes. This method definitively links a variety of conserved and mobile genomic features, and can be extended to further resolve diverse elements present in the human microbiota.

Honey Bee Larval and Adult Microbiome Life Stages Are Effectively Decoupled with Vertical Transmission Overcoming Early Life Perturbations

Microbiomes provide a range of benefits to their hosts which can lead to the coevolution of a joint ecological niche. However, holometabolous insects, some of the most successful organisms on Earth, occupy different niches throughout development, with larvae and adults being physiologically and morphologically highly distinct. Furthermore, transition between the stages usually involves the loss of the gut microbiome since the gut is remodeled during pupation. Most eusocial organisms appear to have evolved a workaround to this problem by sharing their communal microbiome across generations. However, whether this vertical microbiome transmission can overcome perturbations of the larval microbiome remains untested. Honey bees have a relatively simple, conserved, coevolved adult microbiome which is socially transmitted and affects many aspects of their biology. In contrast, larval microbiomes are more variable, with less clear roles. Here, we manipulated the gut microbiome of in vitro-reared larvae, and after pupation of the larvae, we inoculated the emerged bees with adult microbiome to test whether adult and larval microbiome stages may be coupled (e.g., through immune priming). Larval treatments differed in bacterial composition and abundance, depending on diet, which also drove larval gene expression. Nonetheless, adults converged on the typical core taxa and showed limited gene expression variation. This work demonstrates that honey bee adult and larval stages are effectively microbiologically decoupled, and the core adult microbiome is remarkably stable to early developmental perturbations. Combined with the transmission of the microbiome in early adulthood, this allows the formation of long-term host-microbiome associations. IMPORTANCE This work investigated host-microbiome interactions during a crucial developmental stage-the transition from larvae to adults, which is a challenge to both, the insect host and its microbiome. Using the honey bee as a tractable model system, we showed that microbiome transfer after emergence overrides any variation in the larvae, indicating that larval and adult microbiome stages are effectively decoupled. Together with the reliable vertical transfer in the eusocial system, this decoupling ensures that the adults are colonized with a consistent and derived microbiome after eclosion. Taken all together, our data provide additional support that the evolution of sociality, at least in the honey bee system tested here, is linked with host-microbiome relationships.

The gastrointestinal microbiota in colorectal cancer cell migration and invasion

Colorectal carcinoma is the third most common cancer in developed countries and the second leading cause of cancer-related mortality. Interest in the influence of the intestinal microbiota on CRC emerged rapidly in the past few years, and the close presence of microbiota to the tumour mass creates a unique microenvironment in CRC. The gastrointestinal microbiota secrete factors that can contribute to CRC metastasis by influencing, for example, epithelial-to-mesenchymal transition. Although the role of EMT in metastasis is well-studied, mechanisms by which gastrointestinal microbiota contribute to the progression of CRC remain poorly understood. In this review, we will explore bacterial factors that contribute to the migration and invasion of colorectal carcinoma and the mechanisms involved. Bacteria involved in the induction of metastasis in primary CRC include Fusobacterium nucleatum, Enterococcus faecalis, enterotoxigenic Bacteroides fragilis, Escherichia coli and Salmonella enterica. Examples of prominent bacterial factors secreted by these bacteria include Fusobacterium adhesin A and Bacteroides fragilis Toxin. Most of these factors induce EMT-like properties in carcinoma cells and, as such, contribute to disease progression by affecting cell-cell adhesion, breakdown of the extracellular matrix and reorganisation of the cytoskeleton. It is of utmost importance to elucidate how bacterial factors promote CRC recurrence and metastasis to increase patient survival. So far, mainly animal models have been used to demonstrate this interplay between the host and microbiota. More human-based models are needed to study the mechanisms that promote migration and invasion and mimic the progression and recurrence of CRC.

Bacterial genomic epidemiology with mixed samples

Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on single-colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples.

High-resolution sweep metagenomics using fast probabilistic inference

Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.

Colonized Niche, Evolution and Function Signatures of Bifidobacterium pseudolongum within Bifidobacterial Genus

Background: Although genomic features of various bifidobacterial species have received much attention in the past decade, information on Bifidobacterium pseudolongum was limited. In this study, we retrieved 887 publicly available genomes of bifidobacterial species, and tried to elucidate phylogenetic and potential functional roles of B. pseudolongum within the Bifidobacterium genus. Results: The results indicated that B. pseudolongum formed a population structure with multiple monophyletic clades, and had established associations with different types of mammals. The abundance of B. pseudolongum was inversely correlated with that of the harmful gut bacterial taxa. We also found that B. pseudolongum showed a strictly host-adapted lifestyle with a relatively smaller genome size, and higher intra-species genetic diversity in comparison with the other tested bifidobacterial species. For functional aspects, B. pseudolongum showed paucity of specific metabolic functions, and enrichment of specific enzymes degrading complex plant carbohydrates and host glycans. In addition, B. pseudolongum possessed a unique signature of probiotic effector molecules compared with the other tested bifidobacterial species. The investigation on intra-species evolution of B. pseudolongum indicated a clear evolution trajectory in which considerable clade-specific genes, and variation on genomic diversity by clade were observed. Conclusions: These findings provide valuable information for explaining the host adaptability of B. pseudolongum, its evolutionary role, as well as its potential probiotic effects.

Field-Realistic Tylosin Exposure Impacts Honey Bee Microbiota and Pathogen Susceptibility, Which Is Ameliorated by Native Gut Probiotics

Antibiotics have been applied to honey bee (Apis mellifera) hives for decades to treat Paenibacillus larvae, which causes American foulbrood disease and kills honey bee larvae. One of the few antibiotics approved in apiculture is tylosin tartrate. This study examined how a realistic hive treatment regimen of tylosin affected the gut microbiota of bees and susceptibility to a bacterial pathogen. Tylosin treatment reduced bacterial species richness and phylogenetic diversity and reduced the absolute abundances and strain diversity of the beneficial core gut bacteria Snodgrassella alvi and Bifidobacterium spp. Bees from hives treated with tylosin died more quickly after being fed a bacterial pathogen (Serratia marcescens) in the laboratory. We then tested whether a probiotic cocktail of core bee gut species could bolster pathogen resistance. Probiotic exposure increased survival of bees from both control and tylosin-treated hives. Finally, we measured tylosin tolerance of core bee gut bacteria by plating cultured isolates on media with different tylosin concentrations. We observed highly variable responses, including large differences among strains of both S. alvi and Gilliamella spp. Thus, probiotic treatments using cultured bee gut bacteria may ameliorate harmful perturbations of the gut microbiota caused by antibiotics or other factors. IMPORTANCE The antibiotic tylosin tartrate is used to treat honey bee hives to control Paenibacillus larvae, the bacterium that causes American foulbrood. We found that bees from tylosin-treated hives had gut microbiomes with depleted overall diversity as well as reduced absolute abundances and strain diversity of the beneficial bee gut bacteria Snodgrassella alvi and Bifidobacterium spp. Furthermore, bees from treated hives suffered higher mortality when challenged with an opportunistic pathogen. Bees receiving a probiotic treatment, consisting of a cocktail of cultured isolates of native bee gut bacteria, had increased survival following pathogen challenge. Thus, probiotic treatment with native gut bacteria may ameliorate negative effects of antibiotic exposure.

Multi-omic Characterization of Intraspecies Variation in Laboratory and Natural Environments

Investigation of microbial communities has led to many advances in our understanding of ecosystem function, whether that ecosystem is a subglacial lake or the human gut. Within these communities, much emphasis has been placed on interspecific variation and between-species relationships. However, with current advances in sequencing technology resulting in both the reduction in sequencing costs and the rise of shotgun metagenomic sequencing, the importance of intraspecific variation and within-species relationships is becoming realized. Our group conducts multi-omic analyses to understand how spatial structure and resource availability influence diversification within a species and the potential for long-term coexistence of multiple ecotypes within a microbial community. Here, we present examples of ecotypic variation observed in the lab and in the wild, current challenges faced when investigating intraspecies diversity, and future developments that we expect to define the field over the next 5 years.

Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome

Annotated genome sequences provide valuable insight into the functional capabilities of members of microbial communities. Nevertheless, most studies on the microbiome in animal guts use metagenomic data, hampering the assignment of genes to specific microbial taxa. Here, we make use of the readily culturable bacterial communities in the gut of the fruit fly Drosophila melanogaster to obtain draft genome sequences for 96 isolates from wild flies. These include 81 new de novo assembled genomes, assigned to three orders (Enterobacterales, Lactobacillales, and Rhodospirillales) with 80% of strains identified to species level using average nucleotide identity and phylogenomic reconstruction. Based on annotations by the RAST pipeline, among-isolate variation in metabolic function partitioned strongly by bacterial order, particularly by amino acid metabolism (Rhodospirillales), fermentation, and nucleotide metabolism (Lactobacillales) and arginine, urea, and polyamine metabolism (Enterobacterales). Seven bacterial species, comprising 2-3 species in each order, were well-represented among the isolates and included ≥5 strains, permitting analysis of metabolic functions in the accessory genome (i.e., genes not present in every strain). Overall, the metabolic function in the accessory genome partitioned by bacterial order. Two species, Gluconobacter cerinus (Rhodospirillales) and Lactiplantibacillus plantarum (Lactobacillales) had large accessory genomes, and metabolic functions were dominated by amino acid metabolism (G. cerinus) and carbohydrate metabolism (La. plantarum). The patterns of variation in metabolic capabilities at multiple phylogenetic scales provide the basis for future studies of the ecological and evolutionary processes shaping the diversity of microorganisms associated with natural populations of Drosophila.

Genetic divergence and functional convergence of gut bacteria between the Eastern honey bee Apis cerana and the Western honey bee Apis mellifera

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The inter-species diversity of A. cerana and A. mellifera core gut bacteria was revealed.

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Core bacterial species of A. cerana and A. mellifera are distinctive in function.

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Functional profile of overall gut community of A. cerana and A. mellifera are similar.

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Metabolome showed that A. cerana and A. mellifera gut bacteria have similar metabolic capability.

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A. cerana and A. mellifera core gut bacteria have no strict host specificity.

Introduction

The functional relevance of intra-species diversity in natural microbial communities remains largely unexplored. The guts of two closely related honey bee species, Apis cerana and A. mellifera, are colonised by a similar set of core bacterial species composed of host-specific strains, thereby providing a good model for an intra-species diversity study.

Objectives

We aim to assess the functional relevance of intra-species diversity of A. cerana and A. mellifera gut microbiota.

Methods

Honey bee workers were collected from four regions of China. Their gut microbiomes were investigated by shotgun metagenomic sequencing, and the bacterial compositions were compared at the species level. A cross-species colonisation assay was conducted, with the gut metabolomes being characterised by LC-MS/MS.

Results

Comparative analysis showed that the strain composition of the core bacterial species was host-specific. These core bacterial species presented distinctive functional profiles between the hosts. However, the overall functional profiles of the A. cerana and A. mellifera gut microbiomes were similar; this was further supported by the consistency of the honey bees’ gut metabolome, as the gut microbiota of different honey bee species showed rather similar metabolic profiles in the cross-species colonisation assay. Moreover, this experiment also demonstrated that the gut microbiota of A. cerana and A. mellifera could cross colonise between the two honey bee species.

Conclusion

Our findings revealed functional differences in most core gut bacteria between the guts of A. cerana and A. mellifera, which may be associated with their inter-species diversity. However, the functional profiles of the overall gut microbiomes between the two honey bee species converge, probably as a result of the overlapping ecological niches of the two species. Our findings provide critical insights into the evolution and functional roles of the mutualistic microbiota of honey bees and reveal that functional redundancy could stabilise the gene content diversity at the strain-level within the gut community.

Niche partitioning facilitates coexistence of closely related honey bee gut bacteria

Ecological processes underlying bacterial coexistence in the gut are not well understood. Here, we disentangled the effect of the host and the diet on the coexistence of four closely related Lactobacillus species colonizing the honey bee gut. We serially passaged the four species through gnotobiotic bees and in liquid cultures in the presence of either pollen (bee diet) or simple sugars. Although the four species engaged in negative interactions, they were able to stably coexist, both in vivo and in vitro. However, coexistence was only possible in the presence of pollen, and not in simple sugars, independent of the environment. Using metatranscriptomics and metabolomics, we found that the four species utilize different pollen-derived carbohydrate substrates indicating resource partitioning as the basis of coexistence. Our results show that despite longstanding host association, gut bacterial interactions can be recapitulated in vitro providing insights about bacterial coexistence when combined with in vivo experiments.

Association and Occurrence of Bifidobacterial Phylotypes Between Breast Milk and Fecal Microbiomes in Mother-Infant Dyads During the First 2 Years of Life

Breast milk acts as an intermediary for the transfer of functionally important commensal bacteria from mother to infant, especially for Bifidobacterium that can colonize the infant gut. However, the vast majority of rRNA amplicon-based studies reported the conspicuous intercohort and interindividual variation for the prevalence of Bifidobacterium in breast milk. In order to elucidate whether Bifidobacterium phylotypes persistently co-occured at the species or strain level in mother–breast milk–infant triads, we analyzed collectively the next-generation sequencing (NGS) datasets of bacterial 16S rRNA gene and the Bifidobacterium-specific groEL gene from maternal feces, breast milk, and infant feces in a small yet very homogeneous cohort of 25 healthy Uyghur mother–infant pairs (lactation for 7–720 days) in Kashgar, Xinjiang, China. Overall, 16S rRNA gene analysis showed that microbiome in the newborn gut was closer to that of breast milk in the first 4 months of lactation, and subsequently showed an obvious trend of adulthood at 6–12 months. Based on the BLAST accurate taxonomic result of the representative sequences of all ASVs (amplicon sequencing variants), only three sets of ASVs could be clearly assigned into Bifidobacterium species, whereas the remaining eight sets of ASVs corresponded to four indefinite Bifidobacterium species group. By contrast, the groEL gene dataset was partitioned into 376 ASVs, at least belonging to 13 well-known Bifidobacterium species or subspecies, of which 15 ASVs, annotated to seven well-known Bifidobacterium species or subspecies, showed triadic synchronism in most 23 mother–infant pairs tested. However, several other rare bifidobacterial phylotypes, which were frequently encountered in animals, were found to display no correspondence of the presence between the three ecosystems of mother–infant pairs. Our test results were obviously to support the hypothesis that breast milk acts as an intermediary for the transfer of probiotic commensal bacteria from mother to infant, especially for endosymbiotic Bifidobacterium that can colonize the infant gut. Some oxygen-insensitive exogenous Bifidobacterium phylotypes with a cosmopolitan lifestyle may be indirectly transferred to breast milk and the infant’s intestinal tract through environmental contamination. Thus, the groEL gene proved to be a very effective target for the depth resolution of Bifidobacterium community by high-throughput sequencing technologies.

Impact of Nosema Disease and American Foulbrood on Gut Bacterial Communities of Honeybees Apis mellifera

Honeybees, Apis mellifera, are important pollinators of many economically important crops. However, one of the reasons for their decline is pathogenic infection. Nosema disease and American foulbrood (AFB) disease are the most common bee pathogens that propagate in the gut of honeybees. This study investigated the impact of gut-propagating pathogens, including Nosema ceranae and Paenibacillus larvae, on bacterial communities in the gut of A. mellifera using 454-pyrosequencing. Pyrosequencing results showed that N. ceranae was implicated in the elimination of Serratia and the dramatic increase in Snodgrassella and Bartonella in adult bees' guts, while bacterial communities of P. larvae-infected larvae were not affected by the infection. The results indicated that only N. ceranae had an impact on some core bacteria in the gut of A. mellifera through increasing core gut bacteria, therefore leading to the induction of dysbiosis in the bees' gut.

Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction

Whole metagenomic shotgun (WMS) sequencing has dramatically enhanced our ability to study microbial genomics. The possibility to unveil the genetic makeup of bacteria that cannot be easily isolated has significantly expanded our microbiological horizon. Here, we report an approach aimed at uncovering novel bacterial species by the use of targeted WMS sequencing. Employing in silico data retrieved from metabolic modelling to formulate a chemically defined medium (CDM), we were able to isolate and subsequently sequence the genomes of six putative novel species of bacteria from the gut of non‐human primates.

On a Non-Discrete Concept of Prokaryotic Species

The taxonomic concept of species has received continuous attention. A microbial species as a discrete box contains a limited number of highly similar microorganisms assigned to that taxon, following a polyphasic approach. In the 21st Century, with the advancements of sequencing technologies and genomics, the existence of a huge prokaryotic diversity has become well known. At present, the prokaryotic species might no longer have to be understood as discrete values (such as 1 or 2, by homology to Natural numbers); rather, it is expected that some microorganisms could be potentially distributed (according to their genome features and phenotypes) in between others (such as decimal numbers between 1 and 2; real numbers). We propose a continuous species concept for microorganisms, which adapts to the current knowledge on the huge diversity, variability and heterogeneity existing among bacteria and archaea. Likely, this concept could be extended to eukaryotic microorganisms. The continuous species concept considers a species to be delimited by the distance between a range of variable features following a Gaussian-type distribution around a reference organism (i.e., its type strain). Some potential pros and cons of a continuous concept are commented on, offering novel perspectives on our understanding of the highly diversified prokaryotic world, thus promoting discussion and further investigation in the field.

Inter- and Intra-Species Diversity of Lactic Acid Bacteria in Apis mellifera ligustica Colonies

Lactic acid bacteria could positively affect the health of honey bees, including nutritional supplementation, immune system development and pathogen colonization resistance. Based on these considerations the present study evaluated predominant Lactic Acid Bacteria (LAB) species from beebread as well as from the social stomach and midgut of Apis mellifera ligustica honey bee foragers. In detail, for each compartment, the diversity in species and biotypes was ascertained through multiple culture-dependent approaches, consisting of Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE), 16S rRNA gene sequencing and Randomly Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR). The study of a lactic acid bacteria community, performed with PCR-DGGE and sequence analysis targeting the V1-V3 region of the 16S rRNA gene (rDNA), highlighted the presence of a few species, including Apilactobacillus kunkeei, Lactiplantibacillus plantarum, Fructobacillus fructosus, Levilactobacillus brevis and Lactobacillus delbrueckii subsp. lactis. Depending on the different compartments, diverse levels of biodiversity in species were found. Particularly, a very low inter-species biodiversity was detected in the midgut that was prevalently dominated by the presence of Apilactobacillus kunkeei. On the other hand, the beebread was characterized by a reasonable biodiversity showing the presence of five species and the predominance of Apilactobacillus kunkeei, Lactiplantibacillus plantarum and Fructobacillus fructosus. The RAPD-PCR analysis performed on the three predominant species allowed the differentiation into several biotypes for each species. Moreover, a relationship between biotypes and compartments has been detected and each biotype was able to express a specific biochemical profile. The biotypes that populated the social stomach and midgut were able to metabolize sugars considered toxic for bees while those isolated from beebread could contribute to release useful compounds with functional properties. Based on this knowledge, new biotechnological approaches could be developed to improve the health of honey bees and the quality of bee products.

Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome

The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.

Host-associated microbiomes can be critical for the health and proper development of animals and plants. The answers to many fundamental questions regarding the modes of acquisition and microevolution of microbiome communities remain to be established. Deciphering strain-level dynamics is essential to fully understand how microbial communities evolve, but the forces shaping the strain-level dynamics of microbial communities remain largely unexplored, mostly because of methodological issues and cost. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level diversity. In fact, using this method we were able to confirm strain-level results that have been obtained from whole-genome shotgun sequencing of the honey bee gut microbiome but with a much higher resolution. Importantly, our deep sequencing approach allowed us to explore the impact of low-frequency strains (i.e., cryptic strains) on microbiome dynamics. Results show that cryptic strain diversity is not responsible for the observed variations in microbiome composition across bees. Altogether, the findings revealed new fundamental insights regarding strain dynamics of host-associated microbiomes.

IMPORTANCE The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.

Hydrolytic Profile of the Culturable Gut Bacterial Community Associated With Hermetia illucens

Larvae of the black soldier fly (BSF) Hermetia illucens (L.) convert organic waste into high valuable insect biomass that can be used as alternative protein source for animal nutrition or as feedstock for biodiesel production. Since insect biology and physiology are influenced by the gut microbiome, knowledge about the functional role of BSF-associated microorganisms could be exploited to enhance the insect performance and growth. Although an increasing number of culture-independent studies are unveiling the microbiota structure and composition of the BSF gut microbiota, a knowledge gap remains on the experimental validation of the contribution of the microorganisms to the insect growth and development. We aimed at assessing if BSF gut-associated bacteria potentially involved in the breakdown of diet components are able to improve host nutrition. A total of 193 bacterial strains were obtained from guts of BSF larvae reared on a nutritious diet using selective and enrichment media. Most of the bacterial isolates are typically found in the insect gut, with major representatives belonging to the Gammaproteobacteria and Bacilli classes. The hydrolytic profile of the bacterial collection was assessed on compounds typically present in the diet. Finally, we tested the hypothesis that the addition to a nutritionally poor diet of the two isolates Bacillus licheniformis HI169 and Stenotrophomonas maltophilia HI121, selected for their complementary metabolic activities, could enhance BSF growth. B. licheniformis HI169 positively influenced the larval final weight and growth rate when compared to the control. Conversely, the addition of S. maltophilia HI121 to the nutritionally poor diet did not result in a growth enhancement in terms of larval weight and pupal weight and length in comparison to the control, whereas the combination of the two strains positively affected the larval final weight and the pupal weight and length. In conclusion, we isolated BSF-associated bacterial strains with potential positive properties for the host nutrition and we showed that selected isolates may enhance BSF growth, suggesting the importance to evaluate the effect of the bacterial administration on the insect performance.

Kinetics of Phenol Biodegradation by Heavy Metal Tolerant Rhizobacteria Glutamicibacter nicotianae MSSRFPD35 From Distillery Effluent Contaminated Soils

Biodegradation of phenol using bacteria is recognized as an efficient, environmentally friendly and cost-effective approach for reducing phenol pollutants compared to the current conventional physicochemical processes adopted. A potential phenol degrading bacterial strain Glutamicibacter nicotianae MSSRFPD35 was isolated and identified from Canna indica rhizosphere grown in distillery effluent contaminated sites. It showed high phenol degrading efficiency up to 1117 mg L^–1 within 60 h by the secretion of catechol 1,2-dioxygenase via ortho intradial pathway. The strain MSSRFPD35 possess both the catechol 1,2 dioxygenase and catechol 2,3 dioxygenase coding genes that drive the ortho and meta pathways, but the enzymatic assay revealed that the strain cleaves catechol via ortho pathway. Haldane’s kinetic method was well fit to exponential growth data and the following kinetic parameter was obtained: μ^∗ = 0.574 h^–1, K_i = 268.1, K_s = 20.29 mg L^–1. The true μ_max and S_m were calculated as 0.37 h^–1 and 73.76 mg L^–1, respectively. The Haldane’s constant values were similar to earlier studies and healthy fitness depicted in correlation coefficient value R² of 0.98. Phenol degrading kinetic’s was predicted using Haldane’s model as q_max 0.983, K_i′ 517.5 and K_s′ 9.152. Further, MSSRFPD35 was capable of utilizing different monocyclic and polycyclic aromatic hydrocarbons and to degrade phenol in the presence of different heavy metals. This study for the first time reports high phenol degrading efficiency of G. nicotianae MSSRFPD35 in the presence of toxic heavy metals. Thus, the strain G. nicotianae MSSRFPD35 can be exploited for the bioremediation of phenol and its derivatives polluted environments, co-contaminated with heavy metals.

Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species

Most bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet little is known about the extent to which related microbial communities differ in diversity at this level and which underlying mechanisms may constrain and maintain strain-level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species, Apis mellifera and Apis cerana, which diverged about 6 mya. Although the host species are colonized largely by the same bacterial 16S rRNA phylotypes, we find that their communities are host specific when analyzed with genomic resolution. Moreover, despite their similar ecology, A. mellifera displayed a much higher diversity of strains and functional gene content in the microbiota compared to A. cerana, both per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota genomic diversity of these key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity while displaying similar levels of diversity based on the 16S rRNA gene. Such differences are likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities.

Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species

Most bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet little is known about the extent to which related microbial communities differ in diversity at this level and which underlying mechanisms may constrain and maintain strain-level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species, Apis mellifera and Apis cerana, which diverged about 6 mya. Although the host species are colonized largely by the same bacterial 16S rRNA phylotypes, we find that their communities are host specific when analyzed with genomic resolution. Moreover, despite their similar ecology, A. mellifera displayed a much higher diversity of strains and functional gene content in the microbiota compared to A. cerana, both per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota genomic diversity of these key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity while displaying similar levels of diversity based on the 16S rRNA gene. Such differences are likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities.

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Metagenomics reveals differences in gut microbiota diversity beyond the 16S rRNA gene

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Apis cerana and Apis mellifera harbor distinct species and strains in their gut

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Diversity is much higher in A. mellifera per individual bee and within colonies

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Major differences in functions are related to polysaccharide degradation

Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology

Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species-species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.

Gut Microbiota and Disorders of the Central Nervous System

The gut microbiota, consisting of bacteria, fungi, archaea, viruses, and protozoa, together with their collective genomes (microbiome), plays a key role in immune system development and maturation, gut morphology, and in performing essential metabolic functions. Several factors, including lifestyle, body mass index, diet, antibiotic use, and the environment, influence the balance of the intestinal microbiota, whose alterations (the so-called dysbiosis) in recent years have been associated with the onset and/or progression of neurological and neuropsychiatric disorders. The purpose of this narrative review is to provide an overview of the possible involvement of the microbiota-gut-brain axis in the pathogenesis of diseases of the central nervous system, with a special focus on key issues and common misjudgments on the potential contribution of specific microorganisms.

Interspecies Communication in Holobionts by Non-Coding RNA Exchange

Complex organisms are associations of different cells that coexist and collaborate creating a living consortium, the holobiont. The relationships between the holobiont members are essential for proper homeostasis of the organisms, and they are founded on the establishment of complex inter-connections between all the cells. Non-coding RNAs are regulatory molecules that can also act as communication signals between cells, being involved in either homeostasis or dysbiosis of the holobionts. Eukaryotic and prokaryotic cells can transmit signals via non-coding RNAs while using specific extracellular conveyors that travel to the target cell and can be translated into a regulatory response by dedicated molecular machinery. Within holobionts, non-coding RNA regulatory signaling is involved in symbiotic and pathogenic relationships among the cells. This review analyzes current knowledge regarding the role of non-coding RNAs in cell-to-cell communication, with a special focus on the signaling between cells in multi-organism consortia.

Honeybee gut microbiota dysbiosis in pesticide/parasite co-exposures is mainly induced by Nosema ceranae

Honeybees ensure a key ecosystem service by pollinating many agricultural crops and wild plants. However, in the past few decades, managed bee colonies have been declining in Europe and North America. Researchers have emphasized both parasites and pesticides as the most important factors. Infection by the parasite Nosema ceranae and exposure to pesticides can contribute to gut dysbiosis, impacting the honeybee physiology. Here, we examined and quantified the effects of N. ceranae, the neonicotinoid thiamethoxam, the phenylpyrazole fipronil and the carboxamide boscalid, alone and in combination, on the honeybee gut microbiota. Chronic exposures to fipronil and thiamethoxam alone or combined with N. ceranae infection significantly decreased honeybee survival whereas the fungicide boscalid had no effect on uninfected bees. Interestingly, increased mortality was observed in N. ceranae-infected bees after exposure to boscalid, with synergistic negative effects. Regarding gut microbiota composition, co-exposure to the parasite and each pesticide led to decreased abundance of Alphaproteobacteria, and increased abundance of Gammaproteobacteria. The parasite also induced an increase of bacterial alpha-diversity (species richness). Our findings demonstrated that exposure of honeybees to N. ceranae and/or pesticides play a significant role in colony health and is associated with the establishment of a dysbiotic gut microbiota.

High-resolution sweep metagenomics using fast probabilistic inference

Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.

Cadmium and Selenate Exposure Affects the Honey Bee Microbiome and Metabolome, and Bee-Associated Bacteria Show Potential for Bioaccumulation

Honey bees are important insect pollinators used heavily in agriculture and can be found in diverse environments. Bees may encounter toxicants such as cadmium and selenate by foraging on plants growing in contaminated areas, which can result in negative health effects. Honey bees are known to have a simple and consistent microbiome that conveys many benefits to the host, and toxicant exposure may impact this symbiotic microbial community. We used 16S rRNA gene sequencing to assay the effects that sublethal cadmium and selenate treatments had over 7 days and found that both treatments significantly but subtly altered the composition of the bee microbiome. Next, we exposed bees to cadmium and selenate and then used untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics to show that chemical exposure changed the bees' metabolite profiles and that compounds which may be involved in detoxification, proteolysis, and lipolysis were more abundant in treatments. Finally, we exposed several strains of bee-associated bacteria in liquid culture and found that each strain removed cadmium from its medium but that only Lactobacillus Firm-5 microbes assimilated selenate, indicating the possibility that these microbes may reduce the metal and metalloid burden on their host. Overall, our report shows that metal and metalloid exposure can affect the honey bee microbiome and metabolome and that strains of bee-associated bacteria can bioaccumulate these toxicants.IMPORTANCE Bees are important insect pollinators that may encounter environmental pollution when foraging upon plants grown in contaminated areas. Despite the pervasiveness of pollution, little is known about the effects of these toxicants on honey bee metabolism and their symbiotic microbiomes. Here, we investigated the impact of selenate and cadmium exposure on the gut microbiome and metabolome of honey bees. We found that exposure to these chemicals subtly altered the overall composition of the bees' microbiome and metabolome and that exposure to toxicants may negatively impact both host and microbe. As the microbiome of animals can reduce mortality upon metal or metalloid challenge, we grew bee-associated bacteria in media spiked with selenate or cadmium. We show that some bacteria can remove these toxicants from their media in vitro and suggest that bacteria may reduce metal burden in their hosts.

Effects of Tropilaelaps mercedesae on midgut bacterial diversity of Apis mellifera

Tropilaelaps mercedesae is an ectoparasite of Apis mellifera in Asia and is considered a major threat to honey bee health. Herein, we used the Illumina MiSeq platform 16S rDNA Amplicon Sequencing targeting the V3-V4 regions and analysed the effects on the midgut bacterial communities of honey bees infested with T. mercedesae. The overall bacterial community in honey bees infested with T. mercedesae were observed at different developmental stages. Honey bee core intestinal bacterial genera such as Gilliamella, Lactobacillus and Frischella were detected. Tropilaelapsmercedesae infestation changed the bacterial communities in the midgut of A. mellifera. Tropilaelapsmercedesae-infested pupae had greatly increased relative abundances of Micrococcus and Sphingomonas, whereas T. mercedesae-infested 15-day-old workers had significantly reduced relative abundance of non-core microbes: Corynebacterium, Sphingomonas, Acinetobacter and Enhydrobacter compared to T. mercedesae-infested newly emerged bees. The bacterial community was significantly changed at the various T. mercedesae-infested developmental stages of A. mellifera. Tropilaelapsmercedesae infestation also changed the non-core bacterial community from larvae to newly emerged honey bees. Bacterial communities were significantly different between T. mercedesa-infested and non-mite-infested 15-day-old workers. Lactobacillus was dominant in T. mercedesae-infested 15-day-old workers compared to non-mite-infested 15-day-old workers.

Complete Genome Sequencing and Comparative Genome Characterization of Lactobacillus johnsonii ZLJ010, a Potential Probiotic With Health-Promoting Properties

Lactobacillus johnsonii ZLJ010 is a probiotic strain isolated from the feces of a healthy sow and has putative health-promoting properties. To determine the molecular basis underlying the probiotic potential of ZLJ010 and the genes involved in the same, complete genome sequencing and comparative genome analysis with L. johnsonii ZLJ010 were performed. The ZLJ010 genome was found to contain a single circular chromosome of 1,999,879 bp with a guanine-cytosine (GC) content of 34.91% and encoded 18 ribosomal RNA (rRNA) genes and 77 transfer RNA (tRNA) genes. From among the 1,959 protein coding sequences (CDSs), genes known to confer probiotic properties were identified, including genes related to stress adaptation, biosynthesis, metabolism, transport of amino acid, secretion, and the defense machinery. ZLJ010 lacked complete or partial biosynthetic pathways for amino acids but was predicted to compensate for this with an enhanced transport system and some unique amino acid permeases and peptidases that allow it to acquire amino acids and other precursors exogenously. The comparative genomic analysis of L. johnsonii ZLP001 and seven other available L. johnsonii strains, including L. johnsonii NCC533, FI9785, DPC6026, N6.2, BS15, UMNLJ22, and PF01, revealed 2,732 pan-genome orthologous gene clusters and 1,324 core-genome orthologous gene clusters. Phylogenomic analysis based on 1,288 single copy genes showed that ZLJ010 had a closer relationship with the BS15 from yogurt and DPC6026 from the porcine intestinal tract but was located on a relatively standalone branch. The number of clusters of unique, strain-specific genes ranged from 42 to 185. A total of 219 unique genes present in the genome of L. johnsonii ZLJ010 primarily encoded proteins that are putatively involved in replication, recombination and repair, defense mechanisms, transcription, amino acid transport and metabolism, and carbohydrate transport and metabolism. Two unique prophages were predicted in the ZLJ010 genome. The present study helps us understand the ability of L. johnsonii ZLJ010 to better adapt to the gut environment and also its probiotic functionalities.

Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions

Microdiversity can lead to different ecotypes within the same species. These are assumed to provide stability in time and space to those species. However, the role of microdiversity in the stability of whole microbial communities remains underexplored. Understanding the drivers of microbial community stability is necessary to predict community response to future disturbances. Here, we analyzed 16S rRNA gene amplicons from eight different temperate bog lakes at the 97% OTU and amplicon sequence variant (ASV) levels and found ecotypes within the same OTU with different distribution patterns in space and time. We observed that these ecotypes are adapted to different values of environmental factors such as water temperature and oxygen concentration. Our results showed that the existence of several ASVs within a OTU favored its persistence across changing environmental conditions. We propose that microdiversity aids the stability of microbial communities in the face of fluctuations in environmental factors.