1,720,997 research outputs found
The cost of metabolic interactions in symbioses between insects and bacteria with reduced genomes
Get PDFVarious intracellular bacterial symbionts that provide their host with essential nutrients have much-reduced genomes, attributed largely to genomic decay and relaxed selection. To obtain quantitative estimates of the metabolic function of these bacteria, we reconstructed genome-and transcriptome-informed metabolic models of three xylem-feeding insects that bear two bacterial symbionts with complementary metabolic functions: a primary symbiont, Sulcia, that has codiversified with the insects, and a coprimary symbiont of distinct taxonomic origin and with different degrees of genome reduction in each insect species (Hodgkinia in a cicada, Baumannia in a sharpshooter, and Sodalis in a spittlebug). Our simulations reveal extensive bidirectional flux of multiple metabolites between each symbiont and the host, but near-complete metabolic segregation (i.e., near absence of metabolic cross-feeding) between the two symbionts, a likely mode of host control over symbiont metabolism. Genome reduction of the symbionts is associated with an increased number of host metabolic inputs to the symbiont and also reduced metabolic cost to the host. In particular, Sulcia and Hodgkinia with genomes of ≤0.3 Mb are calculated to recycle ~30 to 80% of host-derived nitrogen to essential amino acids returned to the host, while Baumannia and Sodalis with genomes of ≥0.6 Mb recycle 10 to 15% of host nitrogen. We hypothesize that genome reduction of symbionts may be driven by selection for increased host control and reduced host costs, as well as by the stochastic process of genomic decay and relaxed selection. IMPORTANCE Current understanding of many animal-microbial symbioses involving unculturable bacterial symbionts with much-reduced genomes derives almost entirely from nonquantitative inferences from genome data. To overcome this limitation, we reconstructed multipartner metabolic models that quantify both the metabolic fluxes within and between three xylem-feeding insects and their bacterial symbionts. This revealed near-complete metabolic segregation between cooccurring bacterial symbionts, despite extensive metabolite exchange between each symbiont and the host, suggestive of strict host controls over the metabolism of its symbionts. We extended the model analysis to investigate metabolic costs. The positive relationship between symbiont genome size and the metabolic cost incurred by the host points to fitness benefits to the host of bearing symbionts with small genomes. The multicompartment metabolic models developed here can be applied to other symbioses that are not readily tractable to experimental approaches
Analysing the Expressiveness of Metabolic Networks Representations
No full textIn this work, we explore the expressiveness of three graph-based representations of metabolic networks. We consider Abstract Metabolic Networks (AMNs), metabolic-Directed Acyclic Graphs (m-DAGs) and Reaction Graphs (RGs). These representations form a hierarchical view of the metabolism, AMNs being the most abstract, m-DAGs serving as the intermediate, and RGs being the most detailed. We evaluate their expressiveness for a case study comprising 331 Vertebrates and by using the Weisfeiler-Lehman graph kernel to perform the comparison. The results show that AMNs are not able to discern the various taxonomic groups at the Class level, while m-DAGs and RGs clearly distinguish Mammals, Fishes and Birds. When focusing on Mammals at the Order level, only m-DAGs are partially able to identify some of the taxonomic groups. Moreover, m-DAGs are able to distinguish Primates at the Infraorder level of taxonomy. Based on the obtained results, it emerges that m-DAGs are a good compromise between the amount of network information and the computational effort needed to obtain reliable patterns on the taxonomic clustering of the different organisms
New Insights into the Microbiota of Moth Pests
Get PDFIn recent years, next generation sequencing (NGS) technologies have helped to improve our understanding of the bacterial communities associated with insects, shedding light on their wide taxonomic and functional diversity. To date, little is known about the microbiota of lepidopterans, which includes some of the most damaging agricultural and forest pests worldwide. Studying their microbiota could help us better understand their ecology and offer insights into developing new pest control strategies. In this paper, we review the literature pertaining to the microbiota of lepidopterans with a focus on pests, and highlight potential recurrent patterns regarding microbiota structure and composition
The bacterial community associated to an Italian population of Psacothea hilaris: a preliminary study
No full textThe yellow
-
spotted longicorn beetle,
Psacothea hilaris
(Pascoe)
(Coleoptera Cerambycidae), native to eastern Asia, is an invasive
species for Europe, where it is present since 2005 as a pest of
Morus
and
Ficus
spp. Up to
date, no study on the bacterial comm
u-
nity associated with
P. hilaris
has been carried out. The aim of the present work is to characterize the bacterial community ass
o-
ciated to an Italian population of
P. hilaris
collected on
F. carica
L. through a culture
-
independent method (i.e., 454 pyrosequen
c-
ing) targe
t
ing the 16S rRNA gene. The DNA used for bacterial characterization has been extracted from the whole abdomen of 15
adults (seven males and eight females) sampled on the host plant immediately after their
emergence in Alserio (Como, Italy) b
e-
tween August and September 2012. The sequencing strategy led to a total of
≈
2,350
bacterial 16S rRNA gene sequences that
have been clustered into
141 bacterial operational taxonomic units.
Results shown that t
he bacterial community was dominated by
Prote
o
bacteria (86%) belonging to Oxalobacteraceae and Enterobacteriaceae (respec
tively 36.4% and 34.8%).
Pantoea
resulted
the most abundant genus (28.4%), and the other relevant bacterial genera associated with
P. hilaris
are
Ralstonia
(18.6%),
Meth
y-
lobact
e
rium
(3%),
Lactococcus
(2%) and
Propionibacterium
(1.4%)
Complete genome sequence of rhynchophorus ferrugineus endocytobiont candidatus nardonella dryophthoridicola strain NardRF
Get PDFWe report the complete genome sequence and annotation of “Candidatus Nardonella dryophthoridicola” strain NardRF, obtained by sequencing its host bacteriome, Rhynchophorus ferrugineus, using Oxford Nanopore technology
Acetobacter tropicalis is a major symbiont in the olive fruit fly (Bactrocera oleae)
No full textFollowing cultivation-dependent and -independent techniques, we investigated the microbiota associated
with Bactrocera oleae, one of the major agricultural pests in olive-producing countries. Bacterial 16S rRNA gene
libraries and ultrastructural analyses revealed the presence of several bacterial taxa associated with this
insect, among which Acetobacter tropicalis was predominant. The recent increased detection of acetic acid
bacteria as symbionts of other insect model organisms, such as Anopheles stephensi (G. Favia et al., Proc. Natl.
Acad. Sci. USA 104:9047–9051, 2007) or Drosophila melanogaster (C. R. Cox and M. S. Gilmore, Infect. Immun.
75:1565–1576, 2007), prompted us to investigate the association established between A. tropicalis and B. oleae.
Using an A. tropicalis-specific PCR assay, the symbiont was detected in all insects tested originating from
laboratory stocks or field-collected from different locations in Greece. This acetic acid bacterium was successfully
established in cell-free medium, and typing analyses, carried out on a collection of isolates, revealed that
different A. tropicalis strains are present in fly populations. The capability to colonize and lodge in the digestive
system of both larvae and adults and in Malpighian tubules of adults was demonstrated by using a strain
labeled with a green fluorescent protein
A 2000-Year-Old Bacillus stercoris Strain Sheds Light on the Evolution of Cyclic Antimicrobial Lipopeptide Synthesis
Get PDFSome bacteria (notably the genera Bacillus and Clostridium) have the capacity to form endospores that can survive for millions of years in isolated habitats. The genomes of such ancient bacteria provide unique opportunities to understand bacterial evolution and metabolic capabilities over longer time scales. Herein, we sequenced the genome of a 2000-year-old bacterial strain (Mal05) isolated from intact apple seeds recovered during archaeological excavations of a Roman villa in Italy. Phylogenomic analyses revealed that this strain belongs to the species Bacillus stercoris and that it is placed in an early-branching position compared to most other strains of this species. Similar to other Bacillus species, B. stercoris Mal05 had been previously shown to possess antifungal activity. Its genome encodes all the genes necessary for the biosynthesis of fengycin and surfactin, two cyclic lipopeptides known to play a role in the competition of Bacilli with other microorganisms due to their antimicrobial activity. Comparative genomics and analyses of selective pressure demonstrate that these genes are present in all sequenced B. stercoris strains, despite the fact that they are not under strong purifying selection. Hence, these genes may not be essential for the fitness of these bacteria, but they can still provide a competitive advantage against other microorganisms present in the same environment
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Acetic acid bacteria as symbionts of insects
No full textAcetic acid bacteria (AAB) are being increasingly described as associating with different insect species that rely on sugar-based diets. AAB have been found in several insect orders, among them Diptera, Hemiptera, and Hymenoptera, including several vectors of plant, animal, and human diseases. AAB have been shown to associate with the epithelia of different organs of the host, they are able to move within the insect’s body and to be transmitted horizontally and vertically. Here, we review the ecology of AAB and examine their relationships with different insect models including mosquitoes, leafhoppers, and honey bees. We also discuss the potential use of AAB in symbiont-based control strategies, such as “Trojan-horse” agents, to block the transmission of vector-borne diseases
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