More Like this

1. Global Composition of the Bacteriophage Community in Honey Bees

   https://doi.org/10.1128/msystems.01195-21  

   Busby, Taylor J. ; Miller, Craig R. ; Moran, Nancy A. ; Van Leuven, James T. ( April 2022 , mSystems)

   Gambino, Michela (Ed.)

   ABSTRACT The microbial communities in animal digestive systems are critical for host development and health. They stimulate the immune system during development, synthesize important chemical compounds like hormones, aid in digestion, competitively exclude pathogens, etc. Compared to the bacterial and fungal components of the microbiome, we know little about the temporal and spatial dynamics of bacteriophage communities in animal digestive systems. Recently, the bacteriophages of the honey bee gut were characterized in two European bee populations. Most of the bacteriophages described in these two reports were novel, harbored many metabolic genes in their genomes, and had a community structure that suggests coevolution with their bacterial hosts. To describe the conservation of bacteriophages in bees and begin to understand their role in the bee microbiome, we sequenced the virome of Apis mellifera from Austin, TX, and compared bacteriophage compositions among three locations around the world. We found that most bacteriophages from Austin are novel, sharing no sequence similarity with anything in public repositories. However, many bacteriophages are shared among the three bee viromes, indicating specialization of bacteriophages in the bee gut. Our study, along with the two previous bee virome studies, shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacteriophages that primarily infect four of the dominant bacterial phylotypes in the bee gut. IMPORTANCE Viruses that infect bacteria (bacteriophages) are abundant in the microbial communities that live on and in plants and animals. However, our knowledge of the structure, dynamics, and function of these viral communities lags far behind our knowledge of their bacterial hosts. We sequenced the first bacteriophage community of honey bees from the United States and compared the U.S. honey bee bacteriophage community to those of samples from Europe. Our work is an important characterization of an economically critical insect species and shows how bacteriophage communities can contain highly conserved individuals and be highly variable in composition across a wide geographic range. 

   more » « less
2. Comparative genomics of Lactobacillaceae from the gut of honey bees, Apis mellifera , from the Eastern United States

   https://doi.org/10.1093/g3journal/jkac286  

   Bradford, Emma L ; Wax, Noah ; Bueren, Emma K ; Walke, Jenifer B ; Fell, Richard ; Belden, Lisa K ; Haak, David C ( November 2022 , G3 Genes|Genomes|Genetics)

   Engel, P (Ed.)

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

   more » « less
3. Temperature dependence of parasitic infection and gut bacterial communities in bumble bees

   https://doi.org/10.1111/1462-2920.14805  

   Palmer‐Young, Evan C. ; Ngor, Lyna ; Burciaga Nevarez, Rodrigo ; Rothman, Jason A. ; Raffel, Thomas R. ; McFrederick, Quinn S. ( November 2019 , Environmental Microbiology)

   High temperatures (e.g., fever) and gut microbiota can both influence host resistance to infection. However, effects of temperature‐driven changes in gut microbiota on resistance to parasites remain unexplored. We examined the temperature dependence of infection and gut bacterial communities in bumble bees infected with the trypanosomatid parasiteCrithidia bombi. Infection intensity decreased by over 80% between 21 and 37°C. Temperatures of peak infection were lower than predicted based on parasite growthin vitro, consistent with mismatches in thermal performance curves of hosts, parasites and gut symbionts. Gut bacterial community size and composition exhibited slight but significant, non‐linear, and taxon‐specific responses to temperature. Abundance of total gut bacteria and of Orbaceae, both negatively correlated with infection in previous studies, were positively correlated with infection here. Prevalence of the bee pathogen‐containing family Enterobacteriaceae declined with temperature, suggesting that high temperature may confer protection against diverse gut pathogens. Our results indicate that resistance to infection reflects not only the temperature dependence of host and parasite performance, but also temperature‐dependent activity of gut bacteria. The thermal ecology of gut parasite‐symbiont interactions may be broadly relevant to infectious disease, both in ectothermic organisms that inhabit changing climates, and in endotherms that exhibit fever‐based immunity.

    

   more » « less
4. Mycobacterium Phage Butters-Encoded Proteins Contribute to Host Defense against Viral Attack

   https://doi.org/10.1128/mSystems.00534-20  

   Mageeney, Catherine M. ; Mohammed, Hamidu T. ; Dies, Marta ; Anbari, Samira ; Cudkevich, Netta ; Chen, Yanyan ; Buceta, Javier ; Ware, Vassie C. ( October 2020 , mSystems)

   Alegado, Rosie (Ed.)

   ABSTRACT A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc 2 155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31 , confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems. IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance. 

   more » « less
5. Widespread distribution of prophage-encoded virulence factors in marine Vibrio communities

   https://doi.org/10.1038/s41598-018-28326-9  

   Castillo, Daniel ; Kauffman, Kathryn ; Hussain, Fatima ; Kalatzis, Panos ; Rørbo, Nanna ; Polz, Martin F. ; Middelboe, Mathias ( July 2018 , Scientific Reports)

   Prophages are known to encode important virulence factors in the human pathogenVibrio cholerae. However, little is known about the occurrence and composition of prophage-encoded traits in environmental vibrios. A database of 5,674 prophage-like elements constructed from 1,874Vibriogenome sequences, covering sixty-four species, revealed that prophage-like elements encoding possible properties such as virulence and antibiotic resistance are widely distributed among environmental vibrios, including strains classified as non-pathogenic. Moreover, we found that 45% ofVibriospecies harbored a complete prophage-like element belonging to theInoviridaefamily, which encode the zonula occludens toxin (Zot) previously described in theV.cholerae. Interestingly, thesezot-encoding prophages were found in a variety ofVibriostrains covering both clinical and marine isolates, including strains from deep sea hydrothermal vents and deep subseafloor sediments. In addition, the observation that a spacer from the CRISPR locus in the marine fish pathogenV.anguillarumstrain PF7 had 95% sequence identity with azotgene from theInoviridaeprophage found inV.anguillarumstrain PF4, suggests acquired resistance to inoviruses in this species. Altogether, our results contribute to the understanding of the role of prophages as drivers of evolution and virulence in the marineVibriobacteria.

    

   more » « less