Unclassified Enterobacteriaceae Research Articles

Symbionts in waiting: the dynamics of incipient endosymbiont complementation and replacement in minimal bacterial communities of psyllids

BackgroundObligate bacterial primary (P-) endosymbionts that are maternally inherited and codiverge with hosts are widespread across insect lineages with nutritionally restricted diets. Secondary (S-) endosymbionts are mostly facultative, but in some hosts, they complement P-endosymbiont function and therefore become obligate. Phylogenetic evidence exists for host switching and replacement of S-endosymbionts. The community dynamics that precede endosymbiont replacement and complementation have been little studied across host species, yet they are fundamental to the evolution of endosymbiosis.ResultsWe performed bacterial 16S rRNA gene amplicon sequencing of 25 psyllid species (Hemiptera, Psylloidea) across different developmental stages and ecological niches by focusing on the characterisation of the bacteria other than the universally present P-endosymbiont Carsonella (Gammaproteobacteria). Most species harboured only one dominant representative of diverse gammaproteobacterial S-endosymbionts that was consistently detected across all host individuals and populations (Arsenophonus in eight species, Sodalis or Sodalis-like bacteria in four species, unclassified Enterobacteriaceae in eight species). The identity of this dominant obligate S-endosymbiont varied across closely related host species. Unexpectedly, five psyllid species had two or three co-occurring endosymbiont species other than Carsonella within all host individuals, including a Rickettsiella-like bacterium (Gammaproteobacteria) in one psyllid species. Based on standard and quantitative PCR, all psyllids carried Carsonella, at higher titres than their dominant S-endosymbionts. Some psyllids also had Alphaproteobacteria (Lariskella, Rickettsia, Wolbachia) at varying prevalence. Incidence of other bacteria, including known plant pathogens, was low. Ecological niche of gall-forming, lerp-forming and free-living psyllid species did not impact endosymbiont communities. Two flush-feeding psyllid species had population-specific differences, and this was attributable to the higher endosymbiont diversity in native ranges and the absence of some endosymbionts in invasive ranges.ConclusionsOur data support the hypothesis of strict vertical transmission of minimal core communities of bacteria in psyllids. We also found evidence for S-endosymbiont replacement across closely related psyllid species. Multiple dominant S-endosymbionts present in some host species, including at low titre, constitute potential examples of incipient endosymbiont complementation or replacement. Our multiple comparisons of deep-sequenced minimal insect bacterial communities exposed the dynamics involved in shaping insect endosymbiosis.

Consuming fermented distillers' dried grains with solubles (DDGS) feed reveals a shift in the faecal microbiota of growing and fattening pigs using 454 pyrosequencing

The objective of this study was to investigate pig fed by Bacillus coagulans-fermented distillers' dried grains with solubles (DDGS) on the faecal microbial composition and diversity using 454 pyrosequencing. Healthy crossbred (Duroc×Yorkshire×Landrace) growing and fattening pigs (n=48), with an average initial body weight of 65 kg, were divided into two groups (24 replicates per group; four pens per group; six pigs per pen), and given either DDGS feed as the control, or B. coagulans-fermented DDGS feed as the treatment. Faecal samples were collected on day 0, 7, 14, 21, and 28. DNA was extracted, and the V3–V6 region of the 16S rRNA gene was amplified. The fermented DDGS feed affected the relative abundance of bacteria populations at the phylum, genus, and species levels. At the genus level, the consumption of fermented DDGS feed led to higher relative abundances of faecal Prevotella, Lactobacillus, Clostridium, Bifidobacterium, Roseburia, and Bacillus, and lower relative abundances of faecal Escherichia, Ruminococcus, Dialister, unclassified Lachnospiraceae, unclassified Ruminococcaceae, and unclassified Enterobacteriaceae than in the control. At the species level, the consumption of fermented DDGS feed led to higher relative abundances of faecal Prevotella sp., Lactobacillus johnsonii, Lactobacillus fermentum, Lactobacillus mucosae, Lactobacillus reuteri, Clostridium butyricum, Bifidobacterium sp., and Roseburia sp., and lower relative abundances of faecal Prevotella copri, Escherichia coli, Ruminococcus gnavus, Ruminococcus flavefaciens, and Dialister sp. than in the control. Principal coordinates analysis indicated a distinct separation in the faecal microbial communities of pigs that were fed the fermented and unfermented DDGS feed. Fermented DDGS feed significantly increased the average daily gain (ADG) of pigs, and significantly decreased the average daily feed intake (ADFI) of feed and feed/gain (F/G). Thus, our results demonstrate a beneficial shift in the faecal microbiota of pigs consuming fermented DDGS feed, with potential applications in livestock production.

The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus.

BackgroundDengue virus (DENV) is primarily vectored by the mosquito Aedes aegypti, and is estimated to cause 390 million human infections annually. A novel method for DENV control involves stable transinfection of Ae. aegypti with the common insect endosymbiont Wolbachia, which mediates an antiviral effect. However, the mechanism by which Wolbachia reduces the susceptibility of Ae. aegypti to DENV is not fully understood. In this study we assessed the potential of resident microbiota, which can play important roles in insect physiology and immune responses, to affect Wolbachia-mediated DENV blocking.Methodology/FindingsThe microbiome of Ae. aegypti stably infected with Wolbachia strain wMel was compared to that of Ae. aegypti without Wolbachia, using 16s rDNA profiling. Our results indicate that although Wolbachia affected the relative abundance of several genera, the microbiome of both the Wolbachia-infected and uninfected mosquitoes was dominated by Elizabethkingia and unclassified Enterobacteriaceae. To assess the potential of the resident microbiota to affect the Wolbachia-mediated antiviral effect, we used antibiotic treatment before infection with DENV by blood-meal. In spite of a significant shift in the microbiome composition in response to the antibiotics, we detected no effect of antibiotic treatment on DENV infection rates, or on the DENV load of infected mosquitoes.Conclusions/SignificanceOur findings indicate that stable infection with Wolbachia strain wMel produces few effects on the microbiome of laboratory-reared Ae. aegypti. Moreover, our findings suggest that the microbiome can be significantly altered without affecting the fundamental DENV blocking phenotype in these mosquitoes. Since Ae. aegypti are likely to encounter diverse microbiota in the field, this is a particularly important result in the context of using Wolbachia as a method for DENV control.

Effects of Bacillus subtilis CSL2 on the composition and functional diversity of the faecal microbiota of broiler chickens challenged with Salmonella Gallinarum

BackgroundThe chicken gastrointestinal tract contains a diverse microbiota whose composition and structure play important roles in gut functionality. In this study, microbial shifts resulting from feed supplementation with Bacillus subtilis CSL2 were evaluated in broilers challenged and unchallenged with Salmonella Gallinarum. To analyse bacterial community composition and functionality, 454 GS-FLX pyrosequencing of 16S rRNA gene amplicons was performed.ResultsThe Quantitative Insights into Microbial Ecology (QIIME) pipeline was used to analyse changes in the faecal microbiota over a 24-h period. A total of 718,204 sequences from broiler chickens were recorded and analysed. At the phylum level, Firmicutes, Bacteroidetes, and Proteobacteria were the predominant bacterial taxa. In Salmonella-infected chickens (SC), Bacteroidetes were more highly abundant compared to control (NC) and Bacillus-treated (BT) chickens. At the genus level, in the NC and BT groups, Lactobacillus was present at high abundance, and the abundance of Turicibacter, unclassified Enterobacteriaceae, and Bacteroides increased in SC broilers. Furthermore, taxon-independent analysis showed that the SC and BT groups were compositionally distinct at the end of the 24-h period. Further analysis of functional properties showed that B. subtilis CSL2 administration increased gut-associated energy supply mechanisms (i.e. carbohydrate transport and metabolism) to maintain a stable microbiota and protect gut integrity.ConclusionsThis study demonstrated that S. Gallinarum infection and B. subtilis CSL2 supplementation in the diet of broiler chickens influenced the diversity, composition, and functional diversity of the faecal microbiota. Moreover, the findings offer significant insights to understand potential mechanisms of Salmonella infection and the mode of action of probiotics in broiler chickens.

Effect of Formula Containing Lactobacillus reuteri DSM 17938 on Fecal Microbiota of Infants Born by Cesarean-Section.

Microbiota modulation by probiotics in infants born by cesarean (C)-section is poorly understood. We aimed at assessing the response of C-section-delivered infant microbiota to a formula containing Lactobacillus reuteri Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM) 17938 and comparing it with that of vaginally delivered infants. Infants delivered by C-section (C) and vaginally (V) were randomized to receive either control formula (CCt, n = 10; VCt, n = 10) or the same formula containing L reuteri (CLr, n = 11; VLr, n = 9) within 72 hours following birth. Stool samples were collected at 2 weeks and 4 months of age. Microbial DNA was extracted, amplified, and pyrosequenced. The phylogenetic profiles of the CLr, VCt, and VLr microbiota were not significantly different at any age but diverged from that of CCt at 2 weeks. Compared with VCt, CCt displayed lower Bifidobacterium and higher Enterobacter, unclassified Enterobacteriaceae, Enterococcus, Clostridium, and unclassified Clostridiaceae relative abundance at 2 weeks, as well as lower Collinsella and higher Enterococcus and Coprococcus abundance at 4 months. The level of most of these taxa was not significantly different between the CLr and the vaginal-delivery groups. Compared with VCt, the only difference observed in VLr microbiota was higher Lactobacillus at the 2 study ages and Coprococcus at 4 months. Our results show that a formula containing L reuteri DSM 17938 does not essentially alter the microbiota in vaginally born infants. In C-section-delivered infants, however, this strain seems to play the role of keystone species by modulating the early development of the microbiota toward the composition found after vaginal delivery.

Persistent Infection by Wolbachia wAlbB Has No Effect on Composition of the Gut Microbiota in Adult Female Anopheles stephensi.

The bacteria in the midgut of Anopheles stephensi adult females from laboratory colonies were studied by sequencing the V4 region of 16S rRNA genes, with respect to three experimental factors: stable or cured Wolbachia infection; sugar or blood diet; and age. Proteobacteria and Bacteroidetes dominated the community [>90% of operational taxonomic units (OTUs)]; most taxa were in the classes Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, and were assigned to Elizabethkingia (46.9%), Asaia (6.4%) and Pseudomonas (6.0%), or unclassified Enterobacteriaceae (37.2%). Bacterial communities were similar between Wolbachia-cured and Wolbachia-infected mosquito lines, indicating that the gut microbiota were not dysregulated in the presence of Wolbachia. The proportion of Enterobacteriaceae was higher in mosquitoes fed a blood meal compared to those provided a sugar meal. Collectively, the bacterial community had a similar structure in older Wolbachia-infected mosquitoes 8 days after the blood meal, as in younger Wolbachia-infected mosquitoes before a blood meal, except that older mosquitoes had a higher proportion of Enterobacteriaceae and lower proportion of Elizabethkingia. Consistent presence of certain predominant bacteria (Elizabethkingia, Asaia, Pseudomonas, and Enterobacteriaceae) suggests they would be useful for paratransgenesis to control malaria infection, particularly when coupled to a Wolbachia-based intervention strategy.

Can closed artificial ecosystem have an impact on insect microbial community? A case study of yellow mealworm (Tenebrio molitor L.)

A case study of the effects of rearing yellow mealworm (Tenebrio molitor L.) in a closed artificial ecosystem on their associated microbial communities is presented. Two groups of T. molitor larvae were reared, one in a controlled environment agricultural ecosystem and another one in an open environment (as a control). Microbial community structures of larval midgut, larval homogenate and frass samples of both groups, and a sample of feed, which was made through the fermentation of plant wastes, were tested by 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiota differences among the two groups and the feed revealed that the diversities of microbial communities in all samples of both groups decreased compared with the feed, with the lowest in midgut of the both groups. Compared with the three samples from the closed ecosystem, those from the open environment had higher abundances of Bacillus, Lactococcus, Weissella, Escherichia and Clostridiaceae. Enterococcus and some unclassified Enterobacteriaceae were identified as the predominant bacteria in samples from the closed ecosystem. The classes Acidobacteria, Planctomycetacia and Sphingobacteria were found in feed, but almost disappeared in the samples of both groups. Possible metabolic and immune effects of the above differences in associated microbial communities on larval growth are discussed. With the aim of improving the rearing efficiency of T. molitor in such a controlled environment agricultural ecosystem, follow-up study would focus on microbial isolation from the midgut of T. molitor for the preparation of probiotics as well as measures of microbial pathogen control.

The significance of clean and dirty animals for bacterial dynamics along the beef chain

This study investigated the bacterial dynamics along the beef chain for clean and dirty cattle in the slaughter and processing lines, using classic quantitative methods and molecular analyses. In addition, the Norwegian national guidelines for Good Hygiene Practices in Norway were evaluated. In these guidelines, cattle presented for slaughter are categorised according to hide cleanliness, resulting in separate processing lines for meat from very dirty animals and reduced prices to farmers. The study was conducted in two commercial abattoirs in Norway. Two groups were compared; 40 visually clean cattle and 40 visually dirty cattle presented for slaughter, with 20 from each group at each abattoir. The same animals were sampled at five sampling sites: hides, carcass surfaces after dehiding, just before chilling, after chilling, and meat trimmings. Meat trimmings were sampled in only one abattoir. Three hundred and sixty samples were collected by swabbing 100cm2 of the brisket area at the first four sampling sites, and sampling 200g of meat trimmings at the fifth site. The results showed that the hides of dirty cattle had more Enterobacteriaceae and higher Aerobic Plate Counts (APC) than visually clean cattle (P<0.05), however there was no significant difference for Escherichia coli. For the other sampling sites, there were no differences between the dirty and the clean group. An effect of chilling/drying of the carcass surfaces was demonstrated by the significant reduction in the number of carcasses on which E. coli and Enterobacteriaceae were detected; from 11% and 39% before chilling to 1% and 16% after chilling, respectively. Enterobacteriaceae and E. coli were detected in only three and one of the meat trimming samples, respectively. Amplification and sequencing of the 16S rRNA gene from 643 Enterobacteriaceae colonies derived from 107 samples demonstrated that Escherichia/Shigella were dominant within this family on the hides. However, after dehiding, after grading, and after chilling, the genera Citrobacter and Enterobacter dominated. The meat trimmings were dominated by the genera Kluyvera, Hafnia, and unclassified Enterobacteriaceae. The relative proportions of Escherichia/Shigella were higher for dirty animals than for clean animals, and were higher on hides than from sampling sites further down the chain (P<0.05). The minor differences in contamination on carcass surfaces and meat trimmings between clean and dirty cattle indicate that separate processing lines in Norwegian abattoirs seem to be unnecessary.

The HLA-DQ2 genotype selects for early intestinal microbiota composition in infants at high risk of developing coeliac disease

ObjectiveIntestinal dysbiosis has been associated with coeliac disease (CD), but whether the alterations are cause or consequence of the disease is unknown. This study investigated whether the human leukocyte antigen...

The communities of tomato (Solanum lycopersicumL.) leaf endophytic bacteria, analyzed by 16S-ribosomal RNA gene pyrosequencing

Endophytic bacterial communities of tomato leaves were analyzed by 16S-rRNA gene pyrosequencing and compared to rhizosphere communities. Leaf endophytes mainly comprised five phyla, among which Proteobacteria was the most represented (90%), followed by Actinobacteria (1,5%), Planctomycetes (1,4%), Verrucomicrobia (1,1%), and Acidobacteria (0,5%). Gammaproteobacteria was the most abundant class of Proteobacteria (84%), while Alphaproteobacteria and Betaproteobacteria represented 12% and 4% of this phylum, respectively. Rarefaction curves for endophytic bacteria saturated at 80 OTUs, indicating a lower diversity as compared to rhizosphere samples (>1700 OTUs). Hierarchical clustering also revealed that leaf endophytic communities strongly differed from rhizospheric ones. Some OTUs assigned to Bacillus, Stenotrophomonas, and Acinetobacter, as well as some unclassified Enterobacteriaceae were specific for the endophytic community, probably representing bacteria specialized in colonizing this niche. On the other hand, some OTUs detected in the leaf endophytic community were also present in the rhizosphere, probably representing soil bacteria that endophytically colonize leaves. As a whole, this study describes the composition of the endophytic bacterial communities of tomato leaves, identifying a variety of genera that could exert multiple effects on growth and health of tomato plants.