Core Microbiota Research Articles

Carry-over effects of Bacillus thuringiensis on tolerant Aedes albopictus mosquitoes

BackgroundThe biological larvicide Bacillus thuringiensis subsp. israelensis (Bti) represents a safe and effective alternative to chemical insecticides for mosquito control. Efficient control of mosquitoes implicates continuous and extensive application of Bti. This massive use of Bti imposes strong selective pressure, but the complex mode of action of the numerous synergistic Bti endotoxins lower the risk of the emergence of resistance. Although resistance to Bti has not been identified at the population level in nature, some larvae can survive Bti exposure, suggesting tolerance mechanisms. Here we investigated whether Bti-tolerant Aedes albopictus larvae experience any fitness costs. We also studied how this tolerance affects different aspects of the phenotype of the emerging adults that could be relevant for arboviral transmission.MethodsWe exposed Ae. albopictus larvae to lethal concentration of Bti and studied the fitness and gut microbiota of tolerant larvae and their adult counterparts. We further compared the transcript abundance of nine key immunity genes in the gut of Bti-tolerant larvae and their emerging adults versus those not exposed to Bti.ResultsOur results showed that Bti exposure has multifaceted impacts on Ae. albopictus mosquitoes during both larval and adult stages. The carry-over effect of Bti exposure on tolerant larvae manifested in reduced adult emergence rate, shorter lifespan, and decreased fecundity. Bti also alters the gut microbiota of both larvae and adults. We observed higher microbial diversity in Bti-tolerant larvae and changes in the richness of core microbiota. Bti infection and the altered microbiota triggered immune responses in the larval and adult guts.ConclusionsThe observed reduction in mosquito fitness and changes in the composition of the microbiota of adults emerging from tolerant larvae could negatively influence mosquito vectorial capacity. Understanding these impacts is crucial for evaluating the broader implications of Bti-based insecticides in mosquito control programs.Graphical

Unveiling Detoxifying Symbiosis and Dietary Influence on the Southern Green Shield Bug Microbiota.

The Southern green shield bug, Nezara viridula, is an invasive piercing and sucking pest insect that feeds on crops and poses a threat to global food production. Insects live in close relationships with microorganisms providing their host with unique capabilities, such as resistance to toxic plant metabolites. In this study, we investigated the resistance to and detoxification of the plant metabolite 3-nitropropionic acid by core and transient members of the N. viridula microbial community. Microbial community members showed a different tolerance to the toxin and we determined that six out of eight strains detoxified 3-nitropropionic acid. Additionally, we determined that 3-nitropropionic acid might interfere with the biosynthesis and transport of L-leucine. Moreover, our study explored the influence of diet on the gut microbial composition of N. viridula, demonstrating that switching to a single-plant diet shifts the abundance of core microbes. In line with this, testing pairwise microbial interactions revealed that core microbiota members support each other and repress the growth of transient microorganisms. With this work, we provide novel insights into the factors shaping the insect gut microbial communities and demonstrate that N. viridula harbours many toxin-degrading bacteria that could support its resistance to plant defences.

Initial abiotic factors as key drivers in core microbe assembly: Regulatory effects on flavor profiles in light-flavor baijiu

Instability in initial abiotic factors of open solid-state fermentation systems can significantly alter Baijiu's flavor profile, but the mechanisms governing microbial interactions and flavor formation remain unclear. This study comprehensively monitored changes in abiotic factors, microbial communities, and flavor profiles across two distinct fermentation processes in a Baijiu distillery, which differed significantly in their management of initial abiotic factors. Our results revealed significant differences in abiotic factors between the two groups, including moisture, ethanol, acidity, glucose, and organic acid levels. The assembly of microbial communities in fermented grains was primarily driven by deterministic processes. The moisture content in the fermentation grains positively affected the growth and metabolism of core microbiota. The rapid proliferation and metabolism of core microbes led to a rapid increase in the acidity of the fermented grains, alongside a significant accumulation of ethyl lactate. This study provides technical support and theoretical guidance for Baijiu production.

Modulation of gut microbiome in response to the combination of Escherichia coli Nissle 1917 and sugars: a pilot study using host-free system reflecting impact on interpersonal microbiome.

The differential effects of probiotic, prebiotic, and synbiotic formulations on human health are dictated by the inter-individual gut microbial profile. The effects of probiotics such as Escherichia coli Nissle 1917 (ECN) on gut microbiota may vary according to the microbiome profiles of individuals and may be influenced by the presence of certain carbohydrates, which can impact microbial community structure and treatment results. Processed fecal samples from donors having contrasting lifestyles, dietary patterns, and disease histories were mixed with 5 × 106 CFU/mL ECN with or without 1% (w/v) sugars (glucose, galactose, or rice starch) in a host-free system. Post-incubation, 16 s rRNA sequencing was performed. Microbial diversity and taxonomic abundance were computed in relation to the probiotic, prebiotic, and synbiotic treatment effects and interpersonal microbiome variance. Baseline gut microbial profiles showed significant inter-individual variations. ECN treatment alone had a limited impact on the inter-personal gut microbial diversity and abundance. Prebiotics caused a substantial enrichment in Actinobacteria, but there were differences in the responses at the order and genus levels, with enrichment shown in Bifidobacterium, Collinsella, and Megasphaera. Subject B exhibited enrichment in Proteobacteria and Cyanobacteria, but subject A showed more diversified taxonomic alterations as a consequence of the synbiotic treatments. Despite negligible difference in the α-diversity, probiotic, prebiotic, and synbiotic treatments independently resulted in distinct segregation in microbial communities at the β-diversity level. The core microbiota was altered only under prebiotic and synbiotic treatment. Significant correlations primarily for minor phyla were identified under prebiotic and synbiotic treatment. The interindividual microbiome composition strongly influences the effectiveness of personalized diet and treatment plans. The responsiveness to dietary strategies varies according to individual microbiome profiles influenced by health, diet, and lifestyle. Therefore, tailored approaches that consider individual microbiome compositions are crucial for maximizing gut health and treatment results.

The Effect of Larval Exposure to Heavy Metals on the Gut Microbiota Composition of Adult Anopheles arabiensis (Diptera: Culicidae).

Anopheles arabiensis is a highly adaptable member of the An. gambiae complex. Its flexible resting behaviour and diverse feeding habits make conventional vector control methods less effective in controlling this species. Another emerging challenge is its adaptation to breeding in polluted water, which impacts various life history traits relevant to epidemiology. The gut microbiota of mosquitoes play a crucial role in their life history, and the larval environment significantly influences the composition of this bacterial community. Consequently, adaptation to polluted breeding sites may alter the gut microbiota of adult mosquitoes. This study aimed to examine how larval exposure to metal pollution affects the gut microbial dynamics of An. arabiensis adults. Larvae of An. arabiensis were exposed to either cadmium chloride or copper nitrate, with larvae reared in untreated water serving as a control. Two laboratory strains (SENN: insecticide unselected, SENN-DDT: insecticide selected) and F1 larvae sourced from KwaZulu-Natal, South Africa, were exposed. The gut microbiota of the adults were sequenced using the Illumina Next Generation Sequencing platform and compared. Larval metal exposure affected alpha diversity, with a more marked difference in beta diversity. There was evidence of core microbiota shared between the untreated and metal-treated groups. Bacterial genera associated with metal tolerance were more prevalent in the metal-treated groups. Although larval metal exposure led to an increase in pesticide-degrading bacterial genera in the laboratory strains, this effect was not observed in the F1 population. In the F1 population, Plasmodium-protective bacterial genera were more abundant in the untreated group compared to the metal-treated group. This study therefore highlights the importance of considering the larval environment when searching for local bacterial symbionts for paratransgenesis interventions.

In-depth characterization of food and environmental microbiomes across different meat processing plants

BackgroundProcessing environments can be an important source of pathogenic and spoilage microorganisms that cross contaminate meat and meat products. The aim of this study was to characterize the microbiome of raw materials, processing environments and end products from 19 facilities producing different meat products.ResultsThe taxonomic profiles of the microbial communities evolved along processing, from raw materials to end products, suggesting that food contact (FC) surfaces play an important role in modulating the microbiome of final products. Some species persisted with the highest relative abundance in raw materials, food processing environments and/or in the final product, including species from the genera Pseudomonas, Staphylococcus, Brochothrix, Acinetobacter and Psychrobacter. Processing environments showed a very diverse core microbiota, partially shared with the products. Pseudomonas fragi and Pseudomonas sp. Lz4W (in all sample and facility types) and Brochothrix thermosphacta, Psychrobacter sp. and Psychrobacter sp. P11F6 (in raw materials, FC surfaces and end products) were prominent members of the core microbiota for all facilities, while Latilactobacillus sakei was found as a dominant species exclusively in end products from the facilities producing fermented sausages. Processing environments showed a higher amount of antimicrobial resistance genes and virulence factors than raw materials and end products. One thousand four hundred twenty-one medium/high-quality metagenome-assembled genomes (MAGs) were reconstructed. Of these, 274 high-quality MAGs (completeness > 90%) corresponded to 210 putative new species, mostly found in processing environments. For two relevant taxa in meat curing and fermentation processes (S. equorum and L. sakei, respectively), phylogenetic variation was observed associated with the specific processing facility under study, which suggests that specific strains of these taxa may be selected in different meat processing plants, likely contributing to the peculiar sensorial traits of the end products produced in them.ConclusionsOverall, our findings provide the most detailed metagenomics-based perspective up to now of the microbes that thrive in meat, meat products and associated environments and open avenues for future research activities to better understand the microbiome functionality and potential contribution to meat quality and safety.BW5-yJYgBWXLb4-yN7W47nVideo

Genetics, age, and diet influence gut bacterial communities and performance of black soldier fly larvae (Hermetia illucens)

BackgroundThe gut microbiota of black soldier fly larvae (BSFL, Hermetia illucens) play a crucial role in recycling various organic waste streams. This capability is linked to the presence of a potential common core microbiota in BSFL. However, subjective thresholds for defining core taxa and the difficulty of separating genetic and environmental influences have prevented a clear consensus in the literature. We analysed the gut bacterial communities of two genetically distinct BSF lines (wild type (WT) and lab-adapted line (LD)) raised on ten different diets based on common agricultural by-products and food waste in Southeast Asia.ResultsHigh-throughput 16S rRNA gene sequencing revealed that gut bacterial communities were significantly influenced by genetics (p = 0.001), diet (plant/meat-dominated; p = 0.001), larval age (p = 0.001), and the interactions between all three (p = 0.002). This led us to investigate both common core taxa and lineage-specific core taxa. At a strict > 97% prevalence threshold, four core taxa were identified: Providencia_A_732258, an unclassified genus within the family Enterococcaceae, Morganella, and Enterococcus_H_360604. A relaxed threshold (> 80% prevalence) extended the core to include other potential common core taxa such as Klebsiella, Proteus, and Scrofimicrobium. Our data suggest that Proteus, Scrofimicrobium, Corynebacterium, Vagococcus_B, Lysinibacillus_304693 (all LD), and Paenibacillus_J_366884 (WT) are lineage-specific rather than members of a common core (> 90% prevalence in either LD or WT, with prevalence significantly different between lines (p ≤ 0.05)). Positive correlations were observed between several core genera and larval performance in LD, typical of a highly optimized lab-adapted line. Interestingly, only members of the genus Providencia appeared to play a crucial role in most aspects of larval performance in both genetic lineages.ConclusionOur study demonstrates that the gut microbiota of BSFL is influenced by genetic factors, diet composition, larval age, and their interactions. We identified a distinct lineage-specific core microbiota, emphasizing genetic background’s role. Future studies should apply a standardized high prevalence threshold of at least > 90% unless there is a valid reason for relaxation or sample exclusion. The consistent association of Providencia spp. with larval performance across both genetic lines highlights their crucial role in the BSFL gut ecosystem.

Effect of Hypoxia on the Gut Microflora of a Facultative Air-Breathing Loach Lepidocephalichthys guntea.

One of the main risks to fish health in an aquatic environment is hypoxia, which can either lead to respiratory failure or the emergence of various diseases in a fish population. This investigation examined the impact of hypoxia on the gut bacteria of a loach, Lepidocephalichthys guntea, which under the dissolve oxygen stress can gulp air from surface and breathe using its posterior intestine. High-throughput sequencing was used to examine the anterior and posterior parts of the gut of L. guntea during both normoxia and hypoxia. According to the community profiling of the gut bacteria, prolonged exposure to hypoxia increased the diversity and abundance of bacteria in the posterior part while decreasing both in the anterior part of the gut. Additionally, for both parts of the gut, the core microbiota showed a significant alteration during hypoxia. In correlation network analysis, a more interactive and intricate network was developed at normoxia. According to the comparative analyses of the gut bacteria, hypoxia causes more pronounced alterations in the posterior gut than the anterior gut at various taxonomic levels. As a consequence of hypoxia, several genera like Aeromonas, Pseudomonas, Plesiomonas, Acinetobacter, and Enterobacter were replaced by Streptococcus, Escherichia-Shigella, Janthinobacterium, and Clostridia. A surge in probiotic genera, including Bifidobacterium, Lactobacillus, Blautia, and Cetobacterium, was also seen. The fatty acid biosynthesis pathway was induced only in hypoxia, although all other metabolic pathways were present in both situations, albeit with fewer hits in hypoxia.

Variation in the gut microbiota during the early developmental stages of common carp (Cyprinus carpio L.) and its correlation with feed and pond water microflora

BackgroundFish gut microbiota undergo dynamic changes under the influence of many factors and play an important role in the nutrition, immunity and development in fish. Although common carp (Cyprinus carpio L.) is an economically important freshwater fish, there are few reports on its gut microbiota changes at different early developmental stages. In the present study, the gut microbiota of common carp during the early developmental stages and its correlation with the feed and pond water flora were studied using the Illumina MiSeq sequencing platform.ResultsThe results showed that the gut microbiota of common carp underwent continuous and mild changes over the development process, and the pond water environment might provide bacterial resources and have a certain influence on the changes in the gut microbiota of common carp. However, host selection pressure played a more important role in shaping the gut microbiota. Although the gut microbiota was affected by many factors, the presence of core microbiota indicated that some bacterial species adapt to the gut microenvironment of common carp and played a role in its growth process.ConclusionsThe dynamic changes of gut microbiota of carp in early development stage were related to the feed, water environment and host selection. The results of this study provide a theoretical basis for healthy farming and disease prevention of common carp.

The microbiota of moon snail egg collars is shaped by host-specific factors.

Moon snails (Family: Naticidae) lay eggs using a mixture of mucus and sediment to form an egg mass commonly referred to as an egg collar. These egg collars do not appear to experience micro-biofouling or predation, and this observation led us to hypothesize that the egg collars possess a chemically rich microbiota that protect the egg collars from pathogens. Herein, we sought to gain an understanding of the bacterial composition of egg collars laid by a single species of moon snails, Neverita delessertiana, by amplifying and sequencing the 16S rRNA gene from the egg collar and sediment samples collected at four distinct geographical regions in southwest Florida. Relative abundance and non-metric multidimensional scaling plots revealed distinct differences in the bacterial composition between the egg collar and sediment samples. In addition, the egg collars had a lower α-diversity than the sediment, with specific genera being significantly enriched in the egg collars. Analysis of microorganisms consistent across two seasons suggests that Flavobacteriaceae make up a large portion of the core microbiota (36%-58% of 16S sequences). We also investigated the natural product potential of the egg collar microbiota by sequencing a core biosynthetic gene, the adenylation domains (ADs), within the gene clusters of non-ribosomal peptide synthetase (NRPS). AD sequences matched multiple modules within known NRPS gene clusters, suggesting that these compounds might be produced within the egg collar system. This study lays the foundation for future studies into the ecological role of the moon snail egg collar microbiota.IMPORTANCEAnimals commonly partner with microorganisms to accomplish essential tasks, including chemically defending the animal host from predation and/or infections. Understanding animal-microbe partnerships and the molecules used by the microbe to defend the animals from pathogens or predation has the potential to lead to new pharmaceutical agents. However, very few of these systems have been investigated. A particularly interesting system is nutrient-rich marine egg collars, which often lack visible protections, and are hypothesized to harbor beneficial microbes that protect the eggs. In this study, we gained an understanding of the bacterial strains that form the core microbiota of moon snail egg collars and gained a preliminary understanding of their natural product potential. This work lays the foundation for future work to understand the ecological role of the core microbiota and to study the molecules involved in chemically defending the moon snail eggs.

Elucidating core microbiota in yellow wine (Huangjiu) through flavor-oriented synthesis and construction of microbial communities

Huangjiu, a traditional Chinese alcoholic beverage with a history spanning thousands of years, holds significant cultural and economic value in China. Despite its importance, the complexity of Huangjiu fermentation and the intricate interactions within its microbial community remain underexplored. This study addresses this gap by identifying the core volatile organic compounds (VOCs) and key microorganisms that define the flavor profile of Huangjiu. We employed HS-SPME-GC–MS along with aroma reconstitution and omission experiments to identify core VOCs, including Isobutanol, Isoamyl alcohol, β-Phenylethanol, and others. Metagenomic sequencing combined with QPCR was used to analyze microbial communities, revealing the temporal and spatial dynamics during fermentation. A synthetic microbial community model was constructed using the core microbes identified: Saccharomyces cerevisiae, Lactobacillus brevis, Saccharopolyspora rectivirgula, Bacillus subtilis, Leuconostoc citreum, Lactobacillus plantarum, Lactobacillus curvatus, Lactobacillus casei, and Aspergillus oryzae. This model successfully replicated Huangjiu’s core VOCs and sensory characteristics, increased alcohol content, and reduced acidity. Our study contributes valuable insights into the microbial influences on Huangjiu quality, paving the way for its enhanced production and providing a foundation for future research in fermented beverages.

Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species.

Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.

Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot

BackgroundMicrobes colonizing each compartment of terrestrial plants are indispensable for maintaining crop health. Although corn stalk rot (CSR) is a severe disease affecting maize (Zea mays) worldwide, the mechanisms underlying host–microbe interactions across vertical compartments in maize plants, which exhibit heterogeneous CSR-resistance, remain largely uncharacterized.ResultsHere, we investigated the microbial communities associated with CSR-resistant and CSR-susceptible maize cultivars using multi-omics analysis coupled with experimental verification. Maize cultivars resistant to CSR reshaped the microbiota and recruited Bacillus species with three phenotypes against Fusarium graminearum including niche pre-emption, potential secretion of antimicrobial compounds, and no inhibition to alleviate pathogen stress. By inducing the expression of Tyrosine decarboxylase 1 (TYDC1), encoding an enzyme that catalyzes the production of tyramine and dopamine, Bacillus isolates that do not directly suppress pathogen infection induced the synthesis of berberine, an isoquinoline alkaloid that inhibits pathogen growth. These beneficial bacteria were recruited from the rhizosphere and transferred to the stems but not grains of the CSR-resistant plants.ConclusionsThe current study offers insight into how maize plants respond to and interact with their microbiome and lays the foundation for preventing and treating soil-borne pathogens.FCn65Jq_7Sh4F-UA4uQM99Video

Oropharyngeal microbiome profiling and its association with age and heart failure in the elderly population from the northernmost province of China.

Respiratory tract infections are the most common triggers for heart failure in elderly people. The healthy respiratory commensal microbiota can prevent invasion by infectious pathogens and decrease the risk of respiratory tract infections. However, upper respiratory tract (URT) microbiome in the elderly is not well understood. To comprehend the profiles of URT microbiota in the elderly, and the link between the microbiome and heart failure, we investigated the oropharyngeal (OP) microbiome of these populations in Heilongjiang Province, located in the North-East of China, a high-latitude and cold area with a high prevalence of respiratory tract infection and heart failure. Taxonomy-based analysis showed that six dominant phyla were represented in the OP microbial profiles. Compared with young adults, the OP in the elderly exhibited a significantly different microbial community, mainly characterized by highly prevalent Streptococcus, unidentified_Saccharibacteria, Veillonella, unidentified_Pre votellaceae, and Neisseria. While unidentified_Prevotellaceae dominated in the young OP microbiome. There was competition for niche dominance between Streptococcus and member of Prevotellaceae in the OP. Correlation analysis revealed that the abundance of unidentified_Saccharibacteria was positive, while Streptococcus was negatively correlated to age among healthy elderly. The bacterial structure and abundance in the elderly with heart failure were much like healthy controls. Certain changes in microbial diversity indicated the potential OP microbial disorder in heart failure patients. These results presented here identify the respiratory tract core microbiota in high latitude and cold regions, and reveal the robustness of OP microbiome in the aged, supplying the basis for microbiome-targeted interventions.IMPORTANCETo date, we still lack available data on the oropharyngeal (OP) microbial communities in healthy populations, especially the elderly, in high latitude and cold regions. A better understanding of the significantly changed respiratory tract microbiota in aging can provide greater insight into characteristics of longevity and age-related diseases. In addition, determining the relationship between heart failure and OP microbiome may provide novel prevention and therapeutic strategies. Here, we compared OP microbiome in different age groups and elderly people with or without heart failure in northeastern China. We found that OP microbial communities are strongly linked to healthy aging. And the disease status of heart failure was not a powerful factor affecting OP microbiome. The findings may provide basic data to reveal respiratory bacterial signatures of individuals in a cold geographic region.

Core Bacterial Taxa Determine Formation of Forage Yield in Fertilized Soil.

Understanding the roles of core bacterial taxa in forage production is crucial for developing sustainable fertilization practices that enhance the soil bacteria and forage yield. This study aims to investigate the impact of different fertilization regimes on soil bacterial community structure and function, with a particular focus on the role of core bacterial taxa in contributing to soil nutrient content and enhancing forage yield. Field experiments and high-throughput sequencing techniques were used to analyze the soil bacterial community structure and function under various fertilization regimes, including six treatments, control with no amendment (CK), double the standard rate of organic manure (T01), the standard rate of organic manure with nitrogen input equal to T04 (T02), half the standard rate of inorganic fertilizer plus half the standard rate of organic manure (T03), the standard rate of inorganic fertilizer reflecting local practice (T04), and double the standard rate of inorganic fertilizer (T05). The results demonstrated that organic manure treatments, particularly T01, significantly increased the forage yield and the diversity of core bacterial taxa. Core taxa from the Actinomycetota, Alphaproteobacteria, and Gammaproteobacteria classes were crucial in enhancing the soil nutrient content, directly correlating with forage yield. Fertilization significantly influenced functions relating to carbon and nitrogen cycling, with core taxa playing central roles. The diversity of core microbiota and soil nutrient levels were key determinants of forage yield variations across treatments. These findings underscore the critical role of core bacterial taxa in agroecosystem productivity and advocate for their consideration in fertilization strategies to optimize forage yield, supporting the shift towards sustainable agricultural practices.

Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment.

Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2cm) and bottom depth (250cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.

16S amplicon-based microbiome biomapping of a commercial broiler hatchery

Hatcheries, where eggs from multiple breeder farms are incubated and hatched before being sent to different broiler farms, represent a nexus point in the commercial production of broilers in the United States. Considering all downstream microbial quality and safety aspects of broiler production (live production, processing, consumer use) can be potentially affected by the hatchery, a better understanding of microbial ecology within commercial hatcheries is essential. Therefore, a commercial broiler hatchery was biomapped using 16S rRNA amplicon-based microbiome analyses of four sample type categories (Air, Egg, Water, Facility) across five different places in the pre-hatch, hatch, and post-hatch areas. While distinct microbiota were found for each sample type category and hatchery area, microbial community analyses revealed that Egg microbiota trended towards clustering with the facility-related samples when moving from the prehatch to post-hatch areas, highlighting the potential effect of the hatchery environment in shaping the pre-harvest broiler-related microbiota. Prevalence analyses revealed 20 ASVs (Core20) present in the core microbiota of all sample types and areas, with each ASV possessing a unique distribution throughout the hatchery. Interestingly, three Enterobacteriaceae ASVs were in the Core20, including Salmonella. Subsequent analyses showed that Salmonella, while a minor prehatch and hatch Core20ASV, dominated the Enterobacteriaceae niche and total microbiota in the chick pad feces in the post-hatch area of the hatchery, and the presence of this Salmonella ASV in the post-hatch feces was associated with swabs of breakroom tables. These findings highlight the complexity of commercial hatchery microbiota, including identifying chick pad feces and breakroom tables as potentially important sampling or disinfection targets for hatchery managers to focus their Salmonella mitigation efforts to reduce loads entering live production farms.

Effects of a supplemented diet containing 7 probiotic strains (Honeybeeotic) on honeybee physiology and immune response: analysis of hemolymph cytology, phenoloxidase activity, and gut microbiome

BackgroundIn this study, a probiotic mixture (Honeybeeotic) consisting of seven bacterial strains isolated from a unique population of honeybees (Apis mellifera ligustica) was used. That honeybee population was located in the Roti Abbey locality of the Marche Region in Italy, an area isolated from human activities, and genetic contamination from other honeybee populations. The aim was to investigate the effects of this probiotic mixture on the innate immunity and intestinal microbiome of healthy common honeybees in two hives of the same apiary. Hive A received a diet of 50% glucose syrup, while hive B received the same syrup supplemented with the probiotics, both administered daily for 1 month. To determine whether the probiotic altered the immune response, phenoloxidase activity and hemolymph cellular subtype count were investigated. Additionally, metagenomic approaches were used to analyze the effects on gut microbiota composition and function, considering the critical role the gut microbiota plays in modulating host physiology.ResultsThe results revealed differences in hemocyte populations between the two hives, as hive A exhibited higher counts of oenocytoids and granulocytes. These findings indicated that the dietary supplementation with the probiotic mixture was safe and well-tolerated. Furthermore, phenoloxidase activity significantly decreased in hive B (1.75 ± 0.19 U/mg) compared to hive A (3.62 ± 0.44 U/mg, p < 0.005), suggesting an improved state of well-being in the honeybees, as they did not require activation of immune defense mechanisms. Regarding the microbiome composition, the probiotic modulated the gut microbiota in hive B compared to the control, retaining core microbiota components while causing both positive and negative variations. Notably, several genes, particularly KEGG genes involved in amino acid metabolism, carbohydrate metabolism, and branched-chain amino acid (BCAA) transport, were more abundant in the probiotic-fed group, suggesting an effective nutritional supplement for the host.ConclusionsThis study advocated that feeding with this probiotic mixture induces beneficial immunological effects and promoted a balanced gut microbiota with enhanced metabolic activities related to digestion. The use of highly selected probiotics was shown to contribute to the overall well-being of the honeybees, improving their immune response and gut health.

Characterization of core microbiota of barley seeds from different continents for origin tracing and quarantine pathogen assessment

Seeds are important microbial vectors, and seed-associated pathogens can be introduced into a country through trade, resulting in yield and quality losses in agriculture. The aim of this study was to characterize the microbial communities associated with barley seeds, and based on which, to develop technical approaches to trace their geographical origins, and to inspect and identify quarantine pathogens. Our analysis defined the core microbiota of barley seed and revealed significant differences in the barley seed-associated microbial communities among different continents, suggesting a strong geographic specificity of the barley seed microbiota. By implementing a machine learning model, we achieved over 95% accuracy in tracing the origin of barley seeds. Furthermore, the analysis of co-occurrence and exclusion patterns provided important insights into the identification of candidate biocontrol agents or microbial inoculants that could be useful in improving barley yield and quality. A core pathogen database was developed, and a procedure for inspecting potential quarantine species associated with barley seed was established. These approaches proved effective in detecting four fungal and three bacterial quarantine species for the first time in the port of China. This study not only characterized the core microbiota of barley seeds but also provided practical approaches for tracing the regional origin of barley and identifying potential quarantine pathogens.

Exploring the influence of fertilization on bacterial community fluctuations in Ulva cultivation

Ulva are green algae known for their biomass accumulation on the coast due to eutrophication. As these algae are able to bioremediate nitrate loadings, they are used as biofilters of enriched waters in aquaculture. Ulva form a holobiont by naturally hosting various microbes, also involved in nitrate metabolism. However, little is known about fluctuations of the Ulva holobiont in fertilized waters over time. We surveyed fluctuations of the bacterial community associated with Ulva lacinulata cultivation, with (enriched, ENR) and without (seawater only, SW) nitrate-based fertilization. Ulva biofilm and cultivation water were regularly collected and contextual parameters (nutrients, temperature, pH) were regularly measured over twelve weeks. Metabarcoding of the 16S rDNA in the biofilm and water compartments revealed that fertilization led to higher alpha-diversity. Diversity patterns indicated that samples clustered together for each compartment in SW or ENR. Fertilization led to a different genus composition in the water after 5 days, and it led to a more even community in the biofilm, from few very dominant genera at the beginning of the experiment to more less dominant genera at the end. The core microbiota in the biofilm common to SW and ENR was mainly composed of genera involved in the host fitness and physiology. Core genera common to SW and ENR in the water were likely beneficiating from the culture conditions. Microbiota's predicted metabolic pathways revealed a heightened capacity for nitrate reduction in ENR. These results may serve as a foundation to understand nitrate loadings impact on Ulva's microbiota in eutrophication conditions.