A curated 16S rRNA reference database for the classification of honeybee and bumblebee gut microbiota

Zhang, Xue; Li, Xingan; Su, Qinzhi; Qina, Cao; Chenyi, Li; Niu, Qingsheng; Zheng, Hao

doi:10.17520/biods.2019021

Cited by 12 publications

(5 citation statements)

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“…Bioinformatic analysis was implemented using Mothur (version 1.40.5; Schloss et al, 2009 ; Kozich et al, 2013 ; Schloss, 2020 ). After primer trimming and quality control, sequences were split into groups corresponding to their taxonomy at the level of species and then assigned to operational taxonomic units (OTUs) at a 1% dissimilarity level based on the reference database consisting of aligned 16S rRNA sequences of our 20 strains ( Supplementary Figure S1 ; Xue et al, 2019 ). Relative abundances were then calculated based on the read numbers.…”

Section: Methodsmentioning

confidence: 99%

Stably transmitted defined microbial community in honeybees preserves Hafnia alvei inhibition by regulating the immune system

et al. 2022

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The gut microbiota of honeybees is highly diverse at the strain level and essential to the proper function and development of the host. Interactions between the host and its gut microbiota, such as specific microbes regulating the innate immune system, protect the host against pathogen infections. However, little is known about the capacity of these strains deposited in one colony to inhibit pathogens. In this study, we assembled a defined microbial community based on phylogeny analysis, the ‘Core-20’ community, consisting of 20 strains isolated from the honeybee intestine. The Core-20 community could trigger the upregulation of immune gene expressions and reduce Hafnia alvei prevalence, indicating immune priming underlies the microbial protective effect. Functions related to carbohydrate utilization and the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS systems) are represented in genomic analysis of the defined community, which might be involved in manipulating immune responses. Additionally, we found that the defined Core-20 community is able to colonize the honeybee gut stably through passages. In conclusion, our findings highlight that the synthetic gut microbiota could offer protection by regulating the host immune system, suggesting that the strain collection can yield insights into host-microbiota interactions and provide solutions to protect honeybees from pathogen infections.

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Section: Methodsmentioning

confidence: 99%

Stably transmitted defined microbial community in honeybees preserves Hafnia alvei inhibition by regulating the immune system

et al. 2022

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“…The taxonomy was assigned based on the curated database for bumblebee gut microbiota (Zhang et al. , 2019). The BIOM file was generated with read counts and taxonomy of features.…”

Section: Methodsmentioning

confidence: 99%

“…The original data used Trimmomatic (Bolger et al, 2014) to filter the quality, used USEARCH (Edgar, 2013) to splice the double-ended reads, and removed the chimera with UCHIME (Edgar et al, 2011) to get a high-quality sequence with 420 bp at 79 000 reads. The taxonomy was assigned based on the curated database for bumblebee gut microbiota (Zhang et al, 2019). The BIOM file was generated with read counts and taxonomy of features.…”

Section: Gut Dna Extraction and 16s Rrna Sequencingmentioning

confidence: 99%

Lactobacillus melliventris promotes hive productivity and immune functionality in Bombus terrestris performance in the greenhouse

Yu,

Liu,

Liu

et al. 2023

Insect Science

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Bumblebees are important pollinators in agricultural ecosystems, but their abundance is declining globally. There is an urgent need to protect bumblebee health and their pollination services. Bumblebees possess specialized gut microbiota with potential to be used as probiotics to help defend at‐risk bumblebee populations. However, evidence for probiotic benefits on bumblebees is lacking. Here, we evaluated how supplementation with Lactobacillus melliventris isolated from bumblebee gut affected the colony development of Bombus terrestris. This native strain colonized robustly and persisted long‐term in bumblebees, leading to a significantly higher quality of offspring. Subsequently, the tyrosine pathway was upregulated in the brain and fat body, while the Wnt and mTOR pathways of the gut were downregulated. Notably, the field experiment in the greenhouse revealed the supplementation of L. melliventris led to a 2.5‐fold increase in the bumblebee survival rate and a more than 10% increase in the number of flowers visited, indicating a better health condition and pollination ability in field conditions. Our study represents a first screening for the potential use of the native gut member, L. melliventris, as probiotic strains in hive supplement for bumblebee breeding, which may be a practical approach to improve immunity and hive health.

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“…The script “qiime diversity core-metrics-phylogenetic” was used to perform Alpha and Beta diversity analyses [21]. The taxonomy of the representative sequences was determined using “qiime feature-classifer classify-sklearn” [21] using a classifier trained on the Silva 16S (release 138) reference database [22] and based on the specific primers that were used for amplification. Taxonomic assignments for poorly classified ASVs were confirmed through manual verification using NCBI blastn [23].…”

Section: Methodsmentioning

confidence: 99%

Testing the effectiveness of a commercially sold probiotic on restoring the gut microbiota of honey bees: a field study

Damico,

Beasley,

Greenstein

et al. 2023

Preprint

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Antibiotic use in apiculture is often necessary to ensure the survival of honey bee colonies. However, beekeepers are faced with the dilemma of needing to combat bacterial brood infections while knowing that antibiotics also kill beneficial bacteria important for bee health. In recent years, bee probiotics have become increasingly purchased by beekeepers because of product claims like, being able to “replenish the microbes lost due to agricultural modifications of honey bees’ environment” or “promote optimal gut health.” Unfortunately, these products have little scientific evidence to support their efficacy, and previous lab experiments have refuted some of their claims. Here, we performed hive-level field experiments to test the effectiveness of SuperDFM-HoneyBee™, the most commonly purchased honey bee probiotic in the United States, on restoring the honey bee gut microbiome after antibiotic treatment. Our results indicated that bees administered the probiotic after antibiotic treatment did not recover their microbiota faster than bees only given the antibiotic treatment. Moreover, the microorganisms in the probiotic supplement were never found in the guts of the worker bee samples, even during active treatment. These results highlight that more basic research is needed to test the efficacy and outcomes of currently available commercial honey bee probiotic supplements

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A curated 16S rRNA reference database for the classification of honeybee and bumblebee gut microbiota

Cited by 12 publications

References 0 publications

Stably transmitted defined microbial community in honeybees preserves Hafnia alvei inhibition by regulating the immune system

Stably transmitted defined microbial community in honeybees preserves Hafnia alvei inhibition by regulating the immune system

Lactobacillus melliventris promotes hive productivity and immune functionality in Bombus terrestris performance in the greenhouse

Testing the effectiveness of a commercially sold probiotic on restoring the gut microbiota of honey bees: a field study

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