scholarly journals New Reference Genome Sequences for 17 Bacterial Strains of the Honey Bee Gut Microbiota

2018 ◽  
Vol 7 (3) ◽  
Author(s):  
Kirsten M. Ellegaard ◽  
Philipp Engel
Keyword(s):  
Gut Microbiota ◽  
Honey Bee ◽  
Honey Bees ◽  
Reference Genome ◽  
Reference Database ◽  
Bacterial Strains ◽  
Genome Sequences ◽  
Content Type ◽  
Future Analysis ◽  
Comprehensive Reference

We sequenced the genomes of 17 strains isolated from the gut of honey bees, including strains representing the genera Lactobacillus, Bifidobacterium, Gilliamella, Snodgrassella, Frischella, and Commensalibacter. These genome sequences represent an important step forward in the development of a comprehensive reference database to aid future analysis of this emerging gut microbiota model.

scholarly journals Genome Sequences of Two Single-Stranded DNA Viruses Identified in Varroa destructor

2018 ◽  
Vol 6 (9) ◽  
Author(s):  
Simona Kraberger ◽  
Gabriel A. Visnovsky ◽  
Ron F. van Toor ◽  
Maketalena F. Male ◽  
Kara Waits ◽  
...  
Keyword(s):  
New Zealand ◽  
Honey Bee ◽  
Honey Bees ◽  
Varroa Destructor ◽  
Genome Sequences ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Content Type ◽  
Pathogenic Viruses ◽  
Parasitic Mite

ABSTRACT Varroa destructor is a ubiquitous and parasitic mite of honey bees, infecting them with pathogenic viruses having a major impact on apiculture. We identified two novel circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses from V. destructor sampled from a honey bee hive near Christchurch in New Zealand.

scholarly journals Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota

2020 ◽  
Vol 117 (13) ◽  
pp. 7355-7362 ◽  
Author(s):  
Germán Bonilla-Rosso ◽  
Théodora Steiner ◽  
Fabienne Wichmann ◽  
Evan Bexkens ◽  
Philipp Engel
Keyword(s):  
Gut Microbiota ◽  
Honey Bee ◽  
Honey Bees ◽  
Interaction Network ◽  
Strain Level ◽  
Bacterial Strains ◽  
High Genetic Diversity ◽  
Host Interactions ◽  
The Core ◽  
Bee Health

The honey bee gut microbiota influences bee health and has become an important model to study the ecology and evolution of microbiota–host interactions. Yet, little is known about the phage community associated with the bee gut, despite its potential to modulate bacterial diversity or to govern important symbiotic functions. Here we analyzed two metagenomes derived from virus-like particles, analyzed the prevalence of the identified phages across 73 bacterial metagenomes from individual bees, and tested the host range of isolated phages. Our results show that the honey bee gut virome is composed of at least 118 distinct clusters corresponding to both temperate and lytic phages and representing novel genera with a large repertoire of unknown gene functions. We find that the phage community is prevalent in honey bees across space and time and targets the core members of the bee gut microbiota. The large number and high genetic diversity of the viral clusters seems to mirror the high extent of strain-level diversity in the bee gut microbiota. We isolated eight lytic phages that target the core microbiota member Bifidobacterium asteroides, but that exhibited different host ranges at the strain level, resulting in a nested interaction network of coexisting phages and bacterial strains. Collectively, our results show that the honey bee gut virome consists of a complex and diverse phage community that likely plays an important role in regulating strain-level diversity in the bee gut and that holds promise as an experimental model to study bacteria–phage dynamics in natural microbial communities.

scholarly journals Draft Genome Sequences of Four Parasaccharibacter apium Strains Isolated from Honey Bees

2018 ◽  
Vol 6 (10) ◽  
Author(s):  
Vanessa Corby-Harris ◽  
Kirk E. Anderson
Keyword(s):  
Honey Bee ◽  
Honey Bees ◽  
Draft Genome ◽  
Ecological Strategies ◽  
Genome Sequences ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

ABSTRACT Parasaccharibacter apium displays multiple ecological strategies in its honey bee host. We sequenced the genomes of four strains found in larvae and the adult gut in order to better understand its ecology and relationship to other Acetobacteraceae . The P. apium genome consists of 2,009,892 bp and 1,830 protein-coding genes.

scholarly journals Draft Genome Sequences of Two Enterobacter cloacae subsp. cloacae Strains Isolated from Australian Hematology Patients with Bacteremia

2017 ◽  
Vol 5 (33) ◽  
Author(s):  
Lex E. X. Leong ◽  
David Shaw ◽  
Lito Papanicolas ◽  
Diana Lagana ◽  
Ivan Bastian ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Draft Genome ◽  
Enterobacter Cloacae ◽  
Opportunistic Pathogen ◽  
Healthy Individuals ◽  
Genome Sequences ◽  
Content Type ◽  
Extended Spectrum ◽  
Genes Encoding

ABSTRACT Enterobacter cloacae is a common member of the gut microbiota in healthy individuals. However, it is also an opportunistic pathogen, capable of causing bacteremia. We report the draft genomes of two Enterobacter cloacae subspecies cloacae strains isolated from hematology patients with bacteremia. Both isolates carry genes encoding extended-spectrum β-lactamases.

scholarly journals Complete Genome Sequences of Five Burkholderia Strains with Biocontrol Activity against Various Lettuce Pathogens

2022 ◽  
Author(s):  
Adrien Biessy ◽  
Marie Ciotola ◽  
Mélanie Cadieux ◽  
Daphné Albert ◽  
Martin Filion
Keyword(s):  
Complete Genome ◽  
Burkholderia Cepacia ◽  
Gene Clusters ◽  
Antimicrobial Compounds ◽  
Bacterial Strains ◽  
Genome Sequences ◽  
Biosynthetic Gene Clusters ◽  
Content Type ◽  
Biocontrol Activity ◽  
Complex Display

Numerous bacterial strains from the Burkholderia cepacia complex display biocontrol activity. Here, we report the complete genome sequences of five Burkholderia strains isolated from soil. Biosynthetic gene clusters responsible for the production of antimicrobial compounds were found in the genome of these strains, which display biocontrol activity against various lettuce pathogens.

scholarly journals Draft Genome Sequences of 14 Lactobacillus, Enterococcus, and Staphylococcus Isolates from the Nasopharynx of Healthy Feedlot Cattle

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Samat Amat ◽  
Devin B. Holman ◽  
Edouard Timsit ◽  
Katherine E. Gzyl ◽  
Trevor W. Alexander
Keyword(s):  
Draft Genome ◽  
Feedlot Cattle ◽  
Enterococcus Hirae ◽  
Bacterial Strains ◽  
Genome Sequences ◽  
Content Type

Here, we present the first draft genome sequences of 14 bacterial strains isolated from the nasopharynx of healthy feedlot cattle. These genomes are from 12 Lactobacillus isolates (L. amylovorus, L. buchneri, L. curvatus, and L. paracasei), 1 Enterococcus hirae isolate, and 1 Staphylococcus chromogenes isolate.

scholarly journals A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations

2017 ◽  
Vol 91 (16) ◽  
Author(s):  
Emily J. Remnant ◽  
Mang Shi ◽  
Gabriele Buchmann ◽  
Tjeerd Blacquière ◽  
Edward C. Holmes ◽  
...  
Keyword(s):  
Disease Management ◽  
Honey Bee ◽  
Small Rna ◽  
Honey Bees ◽  
Rna Viruses ◽  
Viral Diversity ◽  
Colony Losses ◽  
Diverse Range ◽  
Deformed Wing Virus ◽  
Content Type

ABSTRACT Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa. This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management. IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales. Collapsing Varroa-infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral diversity in honey bees, we employed viral metatranscriptomics analyses on three geographically diverse Varroa-resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of diverse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and diversity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.

scholarly journals Silencing the Honey Bee (Apis mellifera) Naked Cuticle Gene (nkd) Improves Host Immune Function and Reduces Nosema ceranae Infections

2016 ◽  
Vol 82 (22) ◽  
pp. 6779-6787 ◽  
Author(s):  
Wenfeng Li ◽  
Jay D. Evans ◽  
Qiang Huang ◽  
Cristina Rodríguez-García ◽  
Jie Liu ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Immune Function ◽  
Honey Bee ◽  
Honey Bees ◽  
Nosema Ceranae ◽  
Negative Regulator ◽  
Mrna Levels ◽  
Content Type ◽  
Bee Disease

ABSTRACTNosema ceranaeis a new and emerging microsporidian parasite of European honey bees,Apis mellifera, that has been implicated in colony losses worldwide. RNA interference (RNAi), a posttranscriptional gene silencing mechanism, has emerged as a potent and specific strategy for controlling infections of parasites and pathogens in honey bees. While previous studies have focused on the silencing of parasite/pathogen virulence factors, we explore here the possibility of silencing a host factor as a mechanism for reducing parasite load. Specifically, we used an RNAi strategy to reduce the expression of a honey bee gene,naked cuticle(nkd), which is a negative regulator of host immune function. Our studies found thatnkdmRNA levels in adult bees were upregulated byN. ceranaeinfection (and thus, the parasite may use this mechanism to suppress host immune function) and that ingestion of double-stranded RNA (dsRNA) specific tonkdefficiently silenced its expression. Furthermore, we found that RNAi-mediated knockdown ofnkdtranscripts inNosema-infected bees resulted in upregulation of the expression of several immune genes (Abaecin,Apidaecin,Defensin-1, andPGRP-S2), reduction ofNosemaspore loads, and extension of honey bee life span. The results of our studies clearly indicate that silencing the hostnkdgene can activate honey bee immune responses, suppress the reproduction ofN. ceranae, and improve the overall health of honey bees. This study represents a novel host-derived therapeutic for honey bee disease treatment that merits further exploration.IMPORTANCEGiven the critical role of honey bees in the pollination of agricultural crops, it is urgent to develop strategies to prevent the colony decline induced by the infection of parasites/pathogens. Targeting parasites and pathogens directly by RNAi has been proven to be useful for controlling infections in honey bees, but little is known about the disease impacts of RNAi silencing of host factors. Here, we demonstrate that knocking down the honey bee immune repressor-encodingnkdgene can suppress the reproduction ofN. ceranaeand improve the overall health of honey bees, which highlights the potential role of host-derived and RNAi-based therapeutics in controlling the infections in honey bees. The information obtained from this study will have positive implications for honey bee disease management practices.

scholarly journals Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group

2017 ◽  
Vol 5 (5) ◽  
Author(s):  
Marie-Hélène Guinebretière ◽  
Valentin Loux ◽  
Véronique Martin ◽  
Pierre Nicolas ◽  
Vincent Sanchis ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Draft Genome ◽  
Bacterial Strains ◽  
Genome Sequences ◽  
Bacillus Cereus Group ◽  
Content Type ◽  
Physiological Diversity

ABSTRACT Bacteria from the Bacillus cereus group exhibit genetic and physiological diversity through different ecotypes. Here, we present the draft genome sequences of 20 bacterial strains belonging to the contrasted psychrotolerant and thermotolerant ecotypes.

scholarly journals Frischella japonica sp. nov., an anaerobic member of the Orbales in the Gammaproteobacteria, isolated from the gut of the eastern honey bee, Apis cerana japonica Fabricius

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Laura A. Wolter ◽  
Shota Suenami ◽  
Ryo Miyazaki
Keyword(s):  
New Species ◽  
Honey Bee ◽  
Honey Bees ◽  
Type Strain ◽  
Type Species ◽  
Apis Cerana ◽  
Content Type ◽  
Link Type ◽  
Isolation And Characterization ◽  
A New Species

The gut of honey bees is characterized by a stable and relatively simple community of bacteria, consisting of seven to ten phylotypes. Two closely related honey bees, Apis mellifera (western honey bee) and Apis cerana (eastern honey bee), show a largely comparable occurrence of those phylotypes, but a distinct set of bacterial species and strains within each bee species. Here, we describe the isolation and characterization of Ac13T, a new species within the rare proteobacterial genus Frischella from A. cerana japonica Fabricius. Description of Ac13T as a new species is supported by low identity of the 16S rRNA gene sequence (97.2 %), of the average nucleotide identity based on orthologous genes (77.5 %) and digital DNA–DNA hybridization relatedness (24.7 %) to the next but far related type strain Frischella perrara PEB0191T, isolated from A. mellifera. Cells of Ac13T are mesophilic and have a mean length of 2–4 µm and a width of 0.5 µm. Optimal growth was achieved in anoxic conditions, whereas growth was not observed in oxic conditions and strongly reduced in microaerophilic environment. Strain Ac13T shares several features with other members of the Orbaceae , such as the major fatty acid profile, the respiratory quinone type and relatively low DNA G+C content, in accordance with its evolutionary relationship. Unlike F. perrara , strain Ac13T is susceptible to a broad range of antibiotics, which could be indicative for an antibiotic-free A. cerana bee keeping. In conclusion, we propose strain Ac13T as a novel species for which we propose the name Frischella japonica sp. nov. with the type strain Ac13T (=NCIMB 15259=JCM 34075).

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