16S Metabarcoding Research Articles

Three-Year Monitoring of Microorganisms' Composition and Concentration in Atmospheric Aerosols of Novosibirsk City and Suburbs.

The atmospheric environment is formed under the influence of local and distant sources as a result of horizontal and vertical transport. In the present work, microbiological analysis of 604 samples of atmospheric aerosol collected in the period from September 2020 to September 2023 at four sites differing in anthropogenic load, located in Novosibirsk and the region, was carried out. Day and night aerosol samples were collected during 12 h every two weeks by filtration using Sartorius reinforced Teflon membranes, then sown on a set of nutrient media. The taxonomic affiliation of the isolated microbial isolates was determined based on phenotypic characteristics and analysis of 16S rRNA gene nucleotide sequences. Changes in the composition and concentration of culturable microorganisms depending on the season, time of day, and site of aerosol sampling were observed. In winter, lower fungi and bacteria of the genera Bacillus, Staphylococcus, Micrococcus dominated with an average concentration from zero to 12.5 CFU/m3 of aerosol. In the warm period, the concentration and diversity of cocci, spore-forming and non-spore-forming bacteria, actinomycetes, and fungi (up to 1970 CFU/m3), among which pathogenic microorganisms were found, increased sharply in aerosols. The use of 16S metabarcoding techniques has greatly expanded the range of aerosols' microbial diversity detectable.

Toxic metals in Amazonian soil modify the bacterial community associated with Diplopoda

Toxic metal pollution in the Amazon is a serious problem that reduces the quality of water, soil, air, and consequently alters communities of fauna, flora, and microbiota, harming human health and well-being. Our aim was to determine the impact of toxic metals on the structure of the bacterial community associated with Diplopoda in the Amazon rainforest. Animals were kept in microcosms contaminated with cadmium (50 mg.kg−1), mercury (35 mg.kg−1) and no toxic metal (control). The intestinal and molting chamber microbiota were accessed by culture-dependent and culture-independent methods (16S metabarcoding). The cultivated strains were identified, and their functional traits evaluated: secretion of enzymes, growth at different pH, resistance to metals and antibiotics, and ability to reduce toxic effects of metals on plants. Our research described Brachyurodesmus albus, a new species of Diplopoda. We obtained 177 isolates distributed in 35 genera and 61 species of bacteria (Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota) associated with the gut and molting chamber of B. albus. Metabarcoding data provided a more robust access to the bacterial community, resulting in 24 phyla, 561 genera and 6792 ASVs. The presence of metal Cd and Hg alters the composition and abundance of bacteria associated with B. albus (PERMANOVA p < 0.05). The microhabitat (gut and molting chamber) harbours bacterial communities that differ in composition and abundance (PERMANOVA p < 0.05). The presence of Cd and Hg alters important metabolic pathways related to the prokaryotic defense system; antimicrobial resistance genes, endocytosis and secretion system, estimated by PICRUSt. Bacteria selected with high resistance to Cd and Hg buffer the toxic effect of metals on tomato seedlings. This work describes B. albus and concludes that its diverse bacterial microbiota is altered by soil contamination by toxic metals, as well as being an important repository for prospecting strains to be applied in bioremediation programs.

Probing the functional significance of wild animal microbiomes using omics data

Abstract Host‐associated microbiomes are thought to play a key role in host physiology and fitness, but this conclusion mainly derives from systems biased towards animal models and humans. While many studies on non‐model and wild animals have characterised the taxonomic diversity of their microbiomes, few have investigated the functional potential of these microbial communities. Functional ‘omics’ approaches, such as metagenomics, metatranscriptomics and metabolomics, represent promising techniques to probe the significance of host‐associated microbiomes in the wild. In this review, we propose to (1) briefly define the main available functional omics tools along with their strengths and limitations, (2) summarise the key advances enabled by omics tools to understand microbiome function in human and animal models, (3) showcase examples of how these methods have already brought invaluable insights into wild host microbiomes and (4) provide guidelines on how to implement these tools to address outstanding questions in the field of wild animal microbiomes. To conclude, we suggest that, building on knowledge derived from cheaper, more traditional approaches (e.g. 16S metabarcoding and qPCR), functional omics tools represent a promising approach to test hypotheses regarding the ecological and evolutionary significance of the resident microbiota in wild animals. Read the free Plain Language Summary for this article on the Journal blog.

Sampling fish gut microbiota - A genome-resolved metagenomic approach.

Despite a surge in microbiota-focused studies in teleosts, few have reported functional data on whole metagenomes as it has proven difficult to extract high biomass microbial DNA from fish intestinal samples. The zebrafish is a promising model organism in functional microbiota research, yet studies on the functional landscape of the zebrafish gut microbiota through shotgun based metagenomics remain scarce. Thus, a consensus on an appropriate sampling method accurately representing the zebrafish gut microbiota, or any fish species is lacking. Addressing this, we systematically tested four methods of sampling the zebrafish gut microbiota: collection of faeces from the tank, the whole gut, intestinal content, and the application of ventral pressure to facilitate extrusion of gut material. Additionally, we included water samples as an environmental control to address the potential influence of the environmental microbiota on each sample type. To compare these sampling methods, we employed a combination of genome-resolved metagenomics and 16S metabarcoding techniques. We observed differences among sample types on all levels including sampling, bioinformatic processing, metagenome co-assemblies, generation of metagenome-assembled genomes (MAGs), functional potential, MAG coverage, and population level microdiversity. Comparison to the environmental control highlighted the potential impact of the environmental contamination on data interpretation. While all sample types tested are informative about the zebrafish gut microbiota, the results show that optimal sample type for studying fish microbiomes depends on the specific objectives of the study, and here we provide a guide on what factors to consider for designing functional metagenome-based studies on teleost microbiomes.

Phaeocystis globosa and diatom blooms promote distinct bacterial communities and associations in a coastal ecosystem.

Phytoplankton and bacteria form the foundation of marine food webs. While most studies on phytoplankton bloom influence on bacteria dynamics focus on diatom-dominated blooms due to their global ecological significance, it is unclear if similar patterns extend to other species that compete with diatoms like Phaeocystis spp. This study aimed to contribute to the understanding of associations between phytoplankton and bacteria in a temperate ecosystem. For this, we studied the dynamics of phytoplankton and bacteria, combining 16S metabarcoding, microscopy, and flow cytometry over 4 years (282 samples). Phytoplankton and bacterial communities were studied throughout the year, particularly during contrasting phytoplankton blooms dominated by the Haptophyte Phaeocystis globosa or diatoms. We applied extended local similarity analysis (eLSA) to construct networks during blooming and non-blooming periods. Overall, the importance of seasonal and species-specific interactions between phytoplankton and bacteria is highlighted. In winter, mixed diatom communities were interconnected with bacteria, indicating a synergistic degradation of diverse phytoplankton-derived substrates. In spring, despite the intensity variations of P. globosa blooms, the composition of bacterial communities remained consistent over several years, suggesting establishing a stable-state environment for bacterial communities. Specific associations between monospecific diatom blooms and bacteria were evidenced in summer.

Dynamics of the viral community on the surface of a French smear-ripened cheese during maturation and persistence across production years.

The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development of different microbial groups such as lactic acid bacteria, fungi, and ripening bacteria. Recent studies indicate that a viral community, mainly composed of bacteriophages, also represents a common and substantial part of the cheese microbiome. However, the composition of this community, its temporal variations, and associations between bacteriophages and their hosts remain poorly characterized. Here, we studied a French smear-ripened cheese by both viral metagenomics and 16S metabarcoding approaches to assess both the succession of phages and bacterial communities on the cheese surface during cheese ripening and their temporal variations in ready-to-eat cheeses over the years of production. We observed a clear transition of the phage community structure during ripening with a decreased relative abundance of viral species (vOTUs) associated with Lactococcus phages, which were replaced by vOTUs associated with phages infecting ripening bacteria such as Brevibacterium, Glutamicibacter, Pseudoalteromonas, and Vibrio. The dynamics of the phage community was strongly associated with bacterial successions observed on the cheese surface. Finally, while some variations in the distribution of phages were observed in ready-to-eat cheeses produced at different dates spanning more than 4 years of production, the most abundant phages were detected throughout. This result revealed the long-term persistence of the dominant phages in the cheese production environment. Together, these findings offer novel perspectives on the ecology of bacteriophages in smear-ripened cheese and emphasize the significance of incorporating bacteriophages in the microbial ecology studies of fermented foods.IMPORTANCEThe succession of diverse microbial populations is critical for ensuring the production of high-quality cheese. We observed a temporal succession of phages on the surface of a smear-ripened cheese, with new phage communities showing up when ripening bacteria start covering this surface. Interestingly, the final phage community of this cheese is also consistent over large periods of time, as the same bacteriophages were found in cheese products from the same manufacturer made over 4 years. This research highlights the importance of considering these bacteriophages when studying the microbial life of fermented foods like cheese.

Behavioral transcriptomic effects of triploidy and probiotic therapy (Bifidobacterium, Lactobacillus, and Lactococcus mixture) on juvenile Chinook salmon (Oncorhynchus tshawytscha).

Aquaculturists use polyploid fish to maximize production albeit with some unintended consequences including compromised behaviors and physiological function. Given benefits of probiotic therapies (e.g., improved immune response, growth, and metabolism), we explored probiotic supplementation (mixture of Bifidobacterium, Lactobacillus, and Lactococcus), to overcome drawbacks. We first examined fish gut bacterial community composition using 16S metabarcoding (via principal coordinate analyses and PERMANOVA) and determined probiotics significantly impacted gut bacteria composition (p = 0.001). Secondly, we examined how a genomic disruptor (triploidy) and diet supplements (probiotics) impact gene transcription and behavioral profiles of hatchery-reared Chinook salmon (Oncorhynchus tshawytscha). Juveniles from four treatment groups (diploid-regular feed, diploid-probiotic feed, triploid-regular feed, and triploid-probiotic feed; n = 360) underwent behavioral assays to test activity, exploration, neophobia, predator evasion, aggression/sociality, behavioral sensitivity, and flexibility. In these fish, transcriptional profiles for genes associated with neural functions (neurogenesis/synaptic plasticity) and biomarkers for stress response and development (growth/appetite) were (i) examined across treatments and (ii) used to describe behavioral phenotypes via principal component analyses and general linear mixed models. Triploids exhibited a more active behavioral profile (p = 0.002), and those on a regular diet had greater Neuropeptide Y transcription (p = 0.02). A growth gene (early growth response protein 1, p = 0.02) and long-term neural development genes (neurogenic differentiation factor, p = 0.003 and synaptysomal-associated protein 25-a, p = 0.005) impacted activity and reactionary profiles, respectively. Overall, our probiotic treatment did not compensate for triploidy. Our research highlights novel applications of behavioral transcriptomics for identifying candidate genes and dynamic, mechanistic associations with complex behavioral repertoires.

16S metabarcoding of the bacterial community of a poultry wastewater treatment plant in the Philippines

16S metabarcoding of the bacterial community of a poultry wastewater treatment plant in the Philippines

Testing 16S Primers for Proper Identification of Cyanobacterial Communities in Small Water Bodies

The majority of investigations on microbial communities from various environments are presently built on culture-independent methods. Many studies point to the pivotal, selective role of primers targeting hypervariable regions of 16S rRNA in the metabarcoding of bacteria, including cyanobacterial communities. The selectivity of primers designed to amplify targeted regions of the 16S rRNA gene, which has been highlighted by many authors, limited effective amplification. Moreover, the type and specificity of the studied material can also negatively influence the results of 16S metabarcoding. Most of the studies of cyanobacterial communities have been performed for planktonic microbial communities that are often represented by common, well-studied species. In this study, we present the results of 16S metabarcoding analysis using three primer pairs—two already well-known and a third designed in this study—that amplify divergent regions of the 16S rRNA gene (V3–V4, V4–V6, V6) for benthic, microbial mat-forming cyanobacteria communities. Such communities can be a source of toxigenic cyanobacterial taxa and should be monitored with adequate primers. The comparison of three primer pairs suggested that those designed within the present study describe the structure and composition of highly heterogeneous cyanobacterial mats’ communities better than the others.

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.

Comparison of the density and composition of bacteria and fungi in the air of anoxic and aeration tanks in the wastewater treatment plant

The bioaerosols from the wastewater treatment plant can be propagated into the air, affecting the health of residents, animals, and plants around the area. This study was conducted to evaluate the density and composition of bioaerosols (bacteria and fungi) in anoxic and aeration tanks of a domestic wastewater treatment plant. Bioaerosol samples were taken by the active method with SKC Biostage. The agar dishes were placed at a height of 1.5 m above the ground. After sample collection, the dishes were incubated at 37 ±1 °C for 24h-48h for bacteria and at 25 ±1 °C for 72h-120h for fungi. Then, these microorganisms were identified by 16S rRNA (16S Metabarcoding) method for bacteria and taxonomy method for fungi. The results showed that the density of bacteria and mold in the anoxic tank ranged from 233.2 ±7.8 to 339.2 ±13.9 CFU/m3 and 91.8 ±3.2 to 197.9 ±10.1 CFU/m3, respectively. Meanwhile, bacterial and mold densities of aeration tank ranged from 275.6 ±10.4 to 424.0 ±17.3 CFU/m3 and 176.7 ±5.8 to 254.4 ±12.1 CFU/m3, respectively. The density of bacteria and mold in the aeration tank is higher than in the anoxic tank. On the other hand, the 16S Metabarcoding analysis for the microbial diversity detects more than 100 species in two tanks, the predominant bacterial species are: Bacillus megaterium (B. megaterium), Bacillus cereus (B. cereus), Staphylococcus sciuri (S. sciuri) and two common fungi Aspergillus tamarii (A. tamarii), and Penicillium rubers (P. rubers). This preliminary survey in Viet Nam reveals the existence and diversity of bioaerosols in the air from the biological treatment tanks of the wastewater treatment plant.

Landfill-mined soil-like fraction (LMSF) use in biopolymer composting: Material pre-treatment, bioaugmentation and agricultural prospects

Polylactic Acid (PLA) based compostable bioplastic films degrade under thermophilic composting conditions. The purpose of our study was to understand whether sample pre-treatment along with bioaugmentation of the degradation matrix could reduce the biodegradation time under a simulated composting environment. Sepcifically, we also explored whether the commercial composts could be replaced by landfill-mined soil-like fraction (LMSF) for the said application. The effect of pre-treatment on the material was analysed by tests like tensile strength analysis, hydrophobicity analysis, morphological analysis, thermal degradation profiling, etc. Subsequently, the degradation experiment was performed in a simulated composting environment following the ASTM D5338 standard, along with bioaugmentation in selected experimental setups. When the novel approach of material pre-treatment and bioaugmentation were applied in combination, the time necessary for 90% degradation was reduced by 27% using compost and by 23% using LMSF. Beyond the improvement in degradation rate, the water holding capacity increased significantly for the degradation matrices. With pH, C: N ratio and microbial diversity tested to be favourable through 16s metabarcoding studies, material pre-treatment and bioaugmentation allow LMSF to not only replace commercial compost in polymer degradation but also find immense application in the agricultural sector of drought-affected areas (for better water retention) after it has been used for PLA degradation.

Characterization of dry-cured ham microbiota at 12 months of seasoning obtained from different rearing strategies using 16S rRNA profiling

In this study, we investigated the microbiota of 72 Italian ham samples collected after 12 months of seasoning. The hams were elaborated from pigs fed different rearing methods, including the traditional restricted medium protein diet chosen as control (C group); restrictive low protein diet (LP group); two ad libitum high-protein diet groups (HP9M group: slaughter at 9 months of age; HP170 group: slaughter at 170 kg). A multi-amplicon 16S metabarcoding approach was used, and a total of 2845 Amplicon Sequence Variants were obtained from the 72 ham samples. Main phyla included: Firmicutes (90.8%), Actinobacteria (6.2%), Proteobacteria (2.7%), and Bacteroidota (0.12%). The most common genera were Staphylococcus, Tetragenococcus, and Brevibacterium. Shannon index for α-diversity was found statistically significant, notably for the HP9M group, indicating higher diversity compared to C. PERMANOVA test on β-diversity showed significant differences in rearing methods between HP170 and C, HP170 and LP, and HP9M vs. C. All three rearing methods revealed associations with characteristic communities: the HP9M group had the highest number of associations, many of which were due to spoilage bacteria, whereas the LP group had the highest number of seasoning-favourable genera.

Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.

Environmental DNA metabarcoding for the detection of the silverlip pearl oyster (Pinctada maxima) offshore of Eighty Mile Beach in northwest Australia

Effective fishery management relies on accurate knowledge of the spatial distribution of stocks of target species to efficiently focus fishing efforts. However, the distribution and abundance of species such as the silverlip pearl oyster (Pinctada maxima) can be difficult to determine with traditional survey methods since populations are patchy, often occur in low densities, and individuals can be quite cryptic, living partially buried in sediment. Environmental DNA is increasingly used to survey marine species and has proven to be particularly useful in detecting rare or elusive organisms. Here, we compared the presence of silverlip pearl oysters detected via eDNA metabarcoding to traditional towed video surveys offshore of Eighty Mile Beach, northwest Australia. Seawater samples were collected at the end of towed video transects and sites were categorised into shallow (<40 m depth) or deep (40 m +) groups. We applied an oyster-specific 16S metabarcoding assay as well as a universal 18S assay to identify potential indicator taxa associated with the presence of pearl oysters. Using the 16S assay, we detected silverlip pearl oysters at three of the 12 sites sampled, and found that eDNA records generally matched towed video transect data, with both survey methods detecting the target species predominantly in inshore waters at depths <40 m. Our results indicate that metabarcoding of seawater eDNA can be applied to detect cryptic species of commercial importance but highlight limitations around detecting organisms at very low abundances.

Large intestinal nutritional and physicochemical parameters from different dog sizes reshape canine microbiota structure and functions in vitro

ABSTRACT Different dog sizes are associated with variations in large intestinal physiology including gut microbiota, which plays a key role in animal health. This study aims to evaluate, using the CANIM-ARCOL (Canine Mucosal Artificial Colon), the relative importance of gut microbes versus physicochemical and nutritional parameters of the canine colonic environment in shaping microbiota structure and functions. CANIM-ARCOL was set up to reproduce nutrient availability, bile acid profiles, colonic pH, and transit time from small, medium, or large dogs according to in vivo data, while bioreactors were all inoculated with a fecal sample collected from medium size dogs (n = 2). Applying different dog size parameters resulted in a positive association between size and gas or SCFA production, as well as distinct microbiota profiles as revealed by 16S Metabarcoding. Comparisons with in vivo data from canine stools and previous in vitro results obtained when CANIM-ARCOL was inoculated with fecal samples from three dog sizes revealed that environmental colonic parameters were sufficient to drive microbiota functions. However, size-related fecal microbes were necessary to accurately reproduce in vitro the colonic ecosystem of small, medium, and large dogs. For the first time, this study provides mechanistic insights on which parameters from colonic ecosystem mainly drive canine microbiota in relation to dog size. The CANIM-ARCOL can be used as a relevant in vitro platform to unravel interactions between food or pharma compounds and canine colonic microbiota, under different dog size conditions. The potential of the model will be extended soon to diseased situations (e.g. chronic enteropathies or obesity).

Study on the concentration, composition, and recovery rate of bacterial bioaerosols after rainfall in Ho Chi Minh City.

Aerosolized microorganisms have become an important factor in assessing air quality. To determine the characteristics of bacterial bioaerosols in air and rainwater, as well as calculate the recovery rate of bacteria after rains in Ho Chi Minh City, our study was performed using the SKC Biostage sampler for airborne bacteria and Plate Count Agar (PCA) medium for bacterial concentration. Subsequently, the study determined the bacterial community composition at the phylum and order levels using the 16S rRNA (16S metabarcoding) method. Before the rain, bacterial concentrations in the air ranged from 263.39 ± 21.00 to 277.39 ± 78.99CFU/m3, and in rainwater 264.89 ± 51.17 to 285.72 ± 28.00CFU/m3. Following rains, the bacterial concentrations decreased to their lowest levels within the first 1-2h and gradually increased thereafter, reaching their peak after 9h for heavy rain and after 12h for light and moderate rains. The bacterial bioaerosols recovery rate was determined to be 100% for light and moderate rains and 94.6% for heavy rain. The change in bacterial concentration after rainfall showed a positive correlation with temperature (r = 0.85) and CO2 concentration (r = 0.70) and a negative correlation with relative humidity (r = - 0.79). Bacterial composition analysis revealed that the Actinobacteria, Firmicutes, and Proteobacteria phyla were dominant and characteristic of the humid tropical climate in Vietnam. Notably, Firmicutes were the most prevalent phylum both before and after rains. The increased prevalence of certain bacterial orders, particularly Staphylococcus, could contribute to the spread of pathogens, particularly foodborne pathogens. In addition to rain, relative humidity contributed to reducing bacterial bioaerosols concentration and their recovery rate after the rain.

Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets.

Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.

A zebrafish model to elucidate the impact of host genes on the microbiota

AbstractEvery host species and organism provides a unique environmental niche contributing to the overall diversity of microbial ecosystems from the intestine of an animal to the oceans and forests of our planet. The study of host–microbiota interactions has long focused on the well‐established effects the microbiota has on its host. In contrast, little focus has been allocated to the role of the host in these intricate interactions. However, understanding the role of the host may well be an essential key to understanding the complexity of the relationship between the host and its microbiota. In this study, we present a model in which the effects of host genes on the microbiota can be elucidated and how such genetic effects may shape host‐associated microbiota. We demonstrate a hologenomic approach implementing the CRISPR/Cas system in the zebrafish model to combine the effects of a host gene with 16S metabarcoding and metabolomics data. We show that knocking out the gene coding for the rate‐limiting enzyme in melanogenesis, tyrosinase (tyr), correlates with changes in the intestinal microbiota of zebrafish and differences in the abundance of specific metabolites illustrating the value of our model for studying the impact of host genes on the composition and function of the intestinal microbiota.

THE EFFECT OF DEXTRANAL ON THE GUT BACTERIOBIOME OF CALVES

Background. The search for more efficient pro- and prebiotics to improve calves’ health, including decreasing the incidence of intestinal infections and increasing biomass production, has been very actual. The effect of prebiotics, however, is poorly, especially as related to gut microbiome biodiversity. &#x0D; The aim of this work was to study the influence of dextranal on the growth of calves and their gut(rectum) bacteriobiome.&#x0D; Materials and Methods. Bacteriobiome composition and structure was assessed in the control group (K, conventional diet) and dextranal-receiving group (D) in 18-20 days aged calves by 16S metabarcoding (V3-V4, Illumina MiSeq).&#x0D; Results. Overall, we found 377 operational taxonomic units (OTU) from 168 genera, 91 families, 55 orders, 30 classes and 11 phyla, with more than the half of the total number of identifies OTUs belonging to the Firmicutes phylum, followed by Bacteroidetes and Actinobacteria. The relative abundance of the phylum-specific nucleotide sequences followed the same order of dominance. Dextranal addition resulted in the increased (11.9 kg/calf, or 15%) of the living body mass of the two-months old calves in group D as compared with group K: consequently, the dextranal-related difference in the calves’ gut bacteriobiome composition and structure can be viewed as beneficial. It primarily concerns the decreased abundance of the opportunistic pathogen Escherichia/Shigella (Gammaproteobacteria) in group D. Overall 73 OTUs, including six dominant ones, were found to be differentially abundant in the groups. However, changes in the relative abundance of some OTUs were difficult to interpret, most likely due to the low strain/species resolution by 16S rRNA gene fragments’ sequences. As for the α- biodiversity, there were no differences between the groups, but the overall trend directed to the increasing α- biodiversity of the calves’ gut bacteriobiome after dextranal treatment.&#x0D; Conclusion. This study reports the first attempt to inventory the gut bacteriobiome of the cattle in the region, and the obtained results provide the basis for a more detailed and taxonomically targeted further research.