16S Ribosomal Gene Sequencing Research Articles

The oral microbial composition and diversity affect the clinical course of palmoplantar pustulosis patients after dental focal infection treatment

BackgroundPalmoplantar pustulosis (PPP) is a chronic pustular dermatosis on the palms and soles. Dental focal infections are known as the major worsening factor for PPP. Recent our study of oral microbiome demonstrated dysbiosis in PPP patients. While almost half of the PPP patients improved after treatment of dental focal infections, a certain number of patients did not improve. ObjectiveTo investigate the oral microbial factors affecting the clinical course of PPP after treatment of dental focal infection. MethodsThe oral microbiota of healthy controls (n = 10), improved (n = 7) and not-improved (n = 6) patients were analyzed by sequencing of bacterial 16S ribosomal RNA gene. ResultsThe UniFrac analysis suggested the differences of oral microbiota between improved and not-improved patients. The prevalence of the phylum Proteobacteria was lower in improved patients than in not-improved patients. When the alpha microbial diversity was assessed by Shannon index, Pielou’s index and the average operational taxonomic units (OTUs), not-improved patients had a lower-diversity microbiota compared to improved patients. The degree of changes of oral microbiota after dental focal infection treatment was higher in improved patients than in not-improved patients. Six genera showed significant correlation with blood test data of PPP patients. ConclusionOur findings suggested that oral microbial compositions and diversity could account for the distinct clinical course of PPP patients after treatment of dental focal infection. Oral microbiome analysis of PPP patients may provide a predictive factor for clinical responsiveness to dental focal infection treatment.

Effects of intestinal flora on the degree of infiltration of tumor-infiltrating lymphocytes in breast cancer

Objective: To investigate whether the abundance or diversity of intestinal flora in breast cancer (BC) patients effects on the degree of tumor infiltration lymphocytes in breast cancer tissues. Methods: Between March 2017 and October 2017, a total of 80 biopsy-confirmed female patients with BC were enrolled in the present study at the Breast Center of the Fourth Hospital of Hebei Medical University (Shijiazhuang, China), age distribution ranged from 37 to 74 years, which were divided into three groups based on the infiltration of tumor-infiltrating lymphocytes, as follows: high infiltration of TILs (TIL-H) 25 cases, medium infiltration of TILs (TIL-M) 34 cases and low infiltration of TILs (TIL-L) 21 cases. DNA of the intestinal flora was determined by Illumina sequencing and taxonomy of 16S ribosomal RNA genes. Compare the differences in the abundance or diversity of intestinal flora between these three groups. The relationship between tumor-infiltrating lymphocytes and clinical characteristics was analyzed by χ2 tested, and the relationship with intestinal flora was analyzed by β diversity. Results: There were 3, 174, 2, 996, and 2, 877 different OUTs in the TIL-H, TIL-M, and TIL-L groups. The β-diversity distribution was statistically significant (weighted UniFrac, P<0.01; unweighted UniFrac, P<0.01) when comparing the three groups (TIL-H vs. TIL-M vs. TIL-L), the differences between TIL-L and TIL-H groups were greatest. Conclusions: The infiltration level of tumor-infiltrating lymphocytes in breast cancer patients was closely related to the diversity of intestinal flora.

The Female Reproductive Tract Microbiome-Implications for Gynecologic Cancers and Personalized Medicine.

The microbial colonization of the lower female reproductive tract has been extensively studied over the past few decades. In contrast, the upper female reproductive tract including the uterine cavity and peritoneum where the ovaries and fallopian tubes reside were traditionally assumed to be sterile under non-pathologic conditions. However, recent studies applying next-generation sequencing of the bacterial 16S ribosomal RNA gene have provided convincing evidence for the existence of an upper female reproductive tract microbiome. While the vaginal microbiome and its importance for reproductive health outcomes has been extensively studied, the microbiome of the upper female reproductive tract and its relevance for gynecologic cancers has been less studied and will be the focus of this article. This targeted review summarizes the pertinent literature on the female reproductive tract microbiome in gynecologic malignancies and its anticipated role in future research and clinical applications in personalized medicine.

Habitats and seasons differentiate the assembly of bacterial communities along a trophic gradient of freshwater lakes

Abstract Freshwater lakes are subject to variable degrees of eutrophication. Within lakes, the planktonic bacterial community (PBC) and sediment bacterial community (SBC) are both significant participants in biogeochemical processes of lake ecosystems. However, how the assembly patterns of bacterial communities vary seasonally along a trophic gradient in freshwater lakes is poorly understood. Here, we collected and analysed water and sediment samples from 13 shallow lakes located in an urban region of China during summer and winter, the trophic states of which ranged from mesotrophic to middle eutrophic in summer and oligo‐mesotrophic to light eutrophic in winter. High‐throughput sequencing of 16S ribosomal RNA genes was used to determine the diversity and composition of bacterial communities. Our results indicated that bacterial communities derived from different habitats and seasons did not exhibit a uniform response to lake trophic states. Linear and nonlinear mixed effect models suggested that the α‐diversity of PBC and SBC, respectively, showed a unimodal and monotonically decreasing trend with increasing eutrophication in summer, whereas that of PBC and SBC, respectively, exhibited no obvious trend or an increased pattern along the trophic gradient in winter. In addition, the taxonomic compositional dissimilarity of the PBC was most significantly related to lake trophic differences in summer. Phylogenetic structure analysis revealed that mostly environmental selection regulated the SBC and PBC in both seasons. Moreover, dispersal limitation and homogenising dispersal contributed more to the assembly of SBC and PBC in both seasons, respectively. Water temperature, associated with seasonal variability, was the most important variable driving the PBC assembly, while sediment pH overwhelmed nutrients in regulating the seasonal patterns of SBC assemblages. Overall, we highlighted that the water and sediments, as well as the seasons, differentiated the diversity patterns and assembly processes of bacterial communities along a trophic gradient of freshwater lakes. Our findings provide novel information for understanding the ecological responses of lacustrine bacterial communities to trophic gradients and seasonal variations. This study also contributes an important reference for predicting the changes of microbial community biodiversity under future scenarios of eutrophication. ​

Detection and molecular characterization of two genetically distinct phytoplasmas associated with mungbean seed pod abortion in Iran

New symptoms including aborted seed pods disease were observed on mungbean (Vigna radiata) plants in the most important growing areas in Iran that was similar to symptoms of phytoplasma disease previously reported from Australia. Thirty samples were collected from symptomatic and non-symptomatic plants, followed by PCR amplification, DNA sequencing, RFLP and phylogenetic analysis of 16S ribosomal RNA gene to detect and identify possible associated phytoplasmas. Results indicated that two different phytoplasmas, related to ‘Candidatus Phytoplasma trifolii’ and ‘Candidatus Phytoplasma aurantifolia’, were associated with different symptomatic plants samples from the same field, mixed infection was not observed in these samples. The sequence analysis results indicated that the nucleotide sequences from mungbean isolates 47 (MT674290), 7 (MT674291) and 32 (MT674292) had 98.8% sequence identity to ‘Candidatus Phytoplasma aurantifolia’ isolate TBBP-H1 (Acc. No: MN565885), while isolates 80 (MT674293) and 25 (MT674294) had 99.8% sequence identity similar to ‘Candidatus Phytoplasma trifolii’ (MF092789). In silico RFLP and phylogenetic analyse of mungbean seed pod abortion (MubSpa) phytoplasma indicated that the associated phytoplasmas belonged to phytoplasmas of subgroups 16SrVI-A and 16SrII-D. To the best of our knowledge, this is the first report of association ‘Ca. P. trifolii’ and ‘Ca. P. aurantifolia’ strains infecting mungbean plants in Iran.

Malakoplakia in the Urinary Bladder of 4 Puppies.

Malakoplakia in humans most often affects the urinary bladder and is characterized by inflammation with von Hansemann-type macrophages, with or without Michaelis-Gutmann bodies, and is frequently associated with Escherichia coli infection. We describe the microscopic features of malakoplakia in the urinary bladder of 4 puppies. In all cases, the lamina propria of the urinary bladder was markedly expanded by sheets of large, round to polygonal macrophages with intracytoplasmic, periodic acid-Schiff-positive granules and granular inclusions, and rare Prussian blue-positive inclusions. Macrophages were positive for CD18 and Iba1. In 2 cases, Michaelis-Gutmann bodies were detected with hematoxylin and eosin stain and were best demonstrated with von Kossa stain. E. coli infection was confirmed in 2 cases with bacterial culture or polymerase chain reaction (PCR) and sequencing of the bacterial 16S ribosomal RNA gene. Transmission electron microscopy of one case demonstrated macrophages with abundant lysosomes, phagolysosomes, and rod-shaped bacteria. Microscopic features were similar to human cases of malakoplakia. In dogs, the light microscopic characteristics of malakoplakia closely resemble granular cell tumors and histiocytic ulcerative colitis.

Antibiotics at birth and later antibiotic courses: effects on gut microbiota

BackgroundIntrapartum antibiotic prophylaxis (IAP) is widely used, but the evidence of the long-term effects on the gut microbiota and subsequent health of children is limited. Here, we compared the impacts of perinatal antibiotic exposure and later courses of antibiotic courses on gut microbiota.MethodsThis was a prospective, controlled cohort study among 100 vaginally delivered infants with different perinatal antibiotic exposures: control (27), IAP (27), postnatal antibiotics (24), and IAP and postnatal antibiotics (22). At 1 year of age, we performed next-generation sequencing of the bacterial 16S ribosomal RNA gene of fecal samples.ResultsExposure to the perinatal antibiotics had a clear impact on the gut microbiota. The abundance of the Bacteroidetes phylum was significantly higher in the control group, whereas the relative abundance of Escherichia coli was significantly lower in the control group. The impact of the perinatal antibiotics on the gut microbiota composition was greater than exposure to later courses of antibiotics (28% of participants).ConclusionsPerinatal antibiotic exposure had a marked impact on the gut microbiota at the age of 1 year. The timing of the antibiotic exposure appears to be the critical factor for the changes observed in the gut microbiota.ImpactInfants are commonly exposed to IAP and postnatal antibiotics, and later to courses of antibiotics during the first year of life.Perinatal antibiotics have been associated with an altered gut microbiota during the first months of life, whereas the evidence regarding the long-term impact is more limited.Perinatal antibiotic exposure had a marked impact on the infant’s gut microbiota at 1 year of age.Impact of the perinatal antibiotics on the gut microbiota composition was greater than that of the later courses of antibiotics at the age of 1 year.

A switch of microbial flora coupled with ontogenetic niche shift in Leptinotarsa decemlineata.

In Leptinotarsa decemlineata, a final-instar wandering larva typically undergoes an ontogenetic niche shift (ONS), from potato plant during the foraging stage to its pupation site below ground. Using high-throughput sequencing of the bacterial 16S ribosomal RNA gene, we determined the hypothesis that the L. decemlineata pupae harbor stage-specific bacteria to meet the physiological requirements for underground habitat. We identified 34 bacterial phyla, comprising 73 classes, 208 orders, 375 families, and 766 genera in the collected specimens. Microbes across phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were enriched in the pupae, while those in the phylum Proteobacteria, Tenericutes, Firmicutes, and Bacteroidetes dominated in the larvae and adults. A total of 18 genera, including Blastococcus, Corynebacterium_1, Gordonia, Microbacterium, Nocardia, Nocardioides, Rhodococcus, Solirubrobacter, Tsukamurella, Enterococcus, Acinetobacter, Escherichia_Shigella, Lysobacter, Pseudomonas, and Stenotrophomonas, were specifically distributed in pupae. Moreover, soil sterilizing removed a major portion of bacteria in pupae. Specifically, both Enterococcus and Pseudomonas were eliminated in the soil sterilizing and antibiotic-fed beetle groups. Furthermore, the pupation rate and fresh pupal weight were similar, whereas the emergence rate and adult weight were decreased in the antibiotic-fed beetles, compared with controls. The results demonstrate that a switch of bacterial communities occurs in the pupae; the pupal-specific bacteria genera are mainly originated from soil; this bacterial biodiversity improves pupa performance in soil. Our results provide new insight into the evolutionary fitness of L. decemlineata to different environmental niches.

Intestinal mucosal microbiota composition of patients with acquired immune deficiency syndrome in Guangzhou, China.

Acquired immune deficiency syndrome, caused by the human immunodeficiency virus (HIV), has been associated with intestinal dysbiosis, which includes an increase in the number of mucosa-associated pathobionts. In the present study, the intestinal mucosal microbiota patterns of HIV-infected patients were compared with those of healthy individuals in a population from Guangzhou, China. The gut microbiota of intestinal mucosal samples from 12 patients with HIV (transmission routes included sex and intravenous drug abuse) was compared with that of 12 healthy age- and sex-matched controls. Gut microbial communities were profiled via sequencing of the bacterial 16S ribosomal RNA genes. Dysbiosis in HIV-infected individuals was characterized by decreased α-diversity, decreased levels of Firmicutes and increased levels of Proteobacteria. Furthermore, low mean counts of Lachnoclostridium, Roseburia, Thauera, Dorea and Roseburia inulinivorans, and high mean counts of Halomonas and Shewanella bacteria, were indicated to be HIV-associated mucosal bacterial alterations. The relative abundance of Fusobacterium and Lachnoclostridium was significantly decreased, while that of Halomonas and Shewanella was significantly increased in patients with sexually transmitted HIV-infection compared with healthy controls. Alterations of the gut microbiota during HIV infection were also indicated to be associated with the route of HIV transmission. Certain bacteria may be potential biomarkers for HIV infection in patients from Guangzhou, China.

Differential study of the Parabramis pekinensis intestinal microbiota according to different habitats and different parts of the intestine

PurposeTo identify the differences in gut bacterial community of Parabramis pekinensis under different growth conditions, and the effect of the diet in a controlled habitat on the community structure, aiming to provide a comprehensive survey of how the gut microbiota in P. pekinensis varies depending on habitat.MethodsA total of 73 P. pekinensis from Yangtze River (W), rivers in the outskirts of Jingjiang (Jiangsu province, China, R), and farms (C) were collected to analyze the intestinal microbiota using high-throughput sequencing of the V3-V4 16S ribosomal RNA gene. We also subdivided the gut into the foregut (F), midgut (M), and hindgut (B) to analyze the differences between them.ResultsThe dominant bacterial phyla in P. pekinensis were Fusobacteria, Firmicutes, Proteobacteria, and Actinobacteria; meanwhile, Cyanobacteria, Bacteroidetes, Chloroflexi, and Verrucomicrobia were also highly abundant. It is worth noting that the abundance of Fusobacteria Cetobacterium was also very high. The abundance and diversity of the intestinal microbiota structure of fish taken from breeding farm were significantly lower than those taken from Yangtze river and Suburban river, and the abundance of Aeromonas in the gut of fish taken from Yangtze river was much higher than that of fish taken from Suburban river. Compared to midgut, foregut and hindgut have similar microbiota structures, but did not differ significantly in them.ConclusionsThe core intestinal microbiota of P. pekinensis is the same to other herbivorous and partially omnivorous fish. There were significant differences in the intestinal microbiota structure of P. pekinensis from different habitats, but no significant differences in the microbiota abundance and diversity between the different parts of the intestine.

16S rDNA metabarcoding of the bacterial community associated with workers of Pheidole rugaticeps Emery (Hymenoptera: Formicidae)

Insect microbiota are receiving increasing attention from researchers, particularly with the continued advances in next generation sequencing (NGS) techniques. However, there is a paucity of data on the microbiota of ants that scavenge around human settlements. In this study, we characterized the bacterial communities of Pheidole rugaticeps Emery that were collected scavenging on other household insects using Illumina MiSeq high-throughput sequencing of the bacterial 16S ribosomal DNA gene. P. rugaticeps DNA was extracted from the insect samples using a HiYield™ Genomic DNA isolation kit according to the manufacturer’s protocols and amplified using polymerase chain reaction (PCR). The PCR products were sequenced with the Illumina MiSeq platform according to the standard protocols to amplify the V3–V4 of the 16S rDNA gene. The results for the 16S rDNA genes were analysed using QIIME 2 Core − 2020.6, and a 16S rDNA metabarcoding dataset was presented. A total of 46,651 reads were obtained from three genomic samples. A total of 368 amplicon sequence variants (ASV) comprising 165 genera were revealed and classified into 17 phyla. Proteobacteria (57.47%) and Firmicutes (33.14%) were the most abundant taxa, while Acinetobacter (37.10%) was the most abundant genus in all three sampling groups. Pathogenic bacteria species, such as Acinetobacter baumannii (15%) and Pseudomonas aeruginosa (2.92%), were identified from P. rugaticeps samples collected from a hospital environment. However, this study recommends more studies on the microbiota of Pheidole ants with different feeding habits and habitats to establish their core microbiome.

Clinical characteristics associated with the properties of gut microbiota in peritoneal dialysis patients.

Gut microbiota alters in patients with end-stage renal disease, which contributes to inflammation, atherosclerosis, and results in increased incidence of cardiovascular diseases. The present study investigated the potential clinical factors, which influence the gut microbial structure and function in patients undergoing peritoneal dialysis (PD). This is a cross-sectional study performed in 81 prevalent PD patients. Gut microbiota was assessed by high throughput sequencing of 16S ribosomal ribonucleic acid gene in fecal samples. Gas chromatography was conducted to measure stool short-chain fat acid (SCFA) concentrations. Demographic parameters and clinical characteristics, including dialysis regimen, residual renal function, nutrition, and inflammation, were retrieved and related to the properties of gut microbiota. PD duration, peritoneal glucose exposure, and estimated glomerulus filtration rate (eGFR) were identified to be associated with microbial variations. Significant separation of microbial composition was shown between patients with short or long PD duration (p = 0.015) and marginal differences were found between patients grouped by different levels of peritoneal glucose exposure (p = 0.056) or residual renal function (p = 0.063). A couple of gut bacteria showed different abundance at amplicon sequencing variant level between these patient groups (p < 0.05). In addition, stool isobutyric and isovaleric acid concentrations were significantly reduced in patients with longer dialysis duration, higher peritoneal glucose exposure, or declined eGFR (p < 0.05). This pilot study demonstrated that long dialysis duration, high peritoneal glucose exposure, and loss of residual renal function were associated with gut microbiota alteration and reduced branched-chain SCFA production in PD patients.

Suppression of High-Fat Diet–Induced Obesity by Platycodon Grandiflorus in Mice Is Linked to Changes in the Gut Microbiota

The root of Platycodon grandiflorus (PG) has a long-standing tradition in the Asian diet and herbal medicine, because of its anti-inflammatory and antiobesity effects. Changes in the gut microbiota can have dietary effects on host health, which suggests a relation between the 2. The aim of our study was to investigate the relation between PG-mediated suppression of obesity and the composition and functioning of the gut microbiota. Six-week-old male C57BL/6J mice were fed either a control diet (CON, 10%kcal from fat), a high-fat diet (HFD, 60%kcal from fat), or a PG-supplemented HFD for 18 wk. PG was administered by oral gavage at 2g · kg body weight-1 · d-1. Body weight and food intake were monitored. Lipid metabolism, inflammation, and intestinal barrier function were determined. Amplicon sequencing of the bacterial 16S ribosomal RNA gene was used to explore gut microbiota structure, and nontargeted metabolomics analysis was performed to investigate metabolite concentrations in fecal samples. We found that PG significantly ameliorated HFD-induced inflammation, recovered intestinal barrier integrity (reduced permeability by 39% , P=0.008), reduced fat accumulation by 26% (P=0.009), and changed the expression of key genes involved in the development of white adipose tissue (P<0.05) in HFD-fed mice to similar levels in CON mice. Moreover, PG attenuated HFD-induced changes in the gut microbiota; it especially increased Allobaculum (7.3-fold, P=0.002) relative to HFD, whereas CON was 15.2-fold of HFD (P=0.002). These changes by PG were associated with an increase in the production of SCFAs (butyrate and propionate, P<0.001) and other carbohydrate-related metabolites known to have a major role in disease suppression. Our study demonstrated that PG beneficially changed the gut microbiota and the gut metabolome in HFD-fed mice, and suggests that the antiobesity effects of PG may be mediated via changes in gut microbiota composition and metabolic activity.

Isolation and Identification of Local Bactria Produced from Soil-Borne Urease

The hydrolysis of urea by the enzyme urease is significant for increasing the irroles in human pathogenicity, biocementation, soil fertilizer, and subsequently in soil improvement. This study devoted to the isolation of urease from urea-rich soil samples collected from seven different locations. Isolation of the various bacterial species was conducted using nutrient agar. The identity of isolated urease was based on morphological characteristics and standard microbiological and biochemical procedures. The urease producing strains of bacteria were obtained using the urease hydrolysis test. The bacterial isolates produced from soil samples collected from different environments and treated by different morphological processes helped in precipitation of large calcium carbonate (CaCO3) crystal aggregates precipitated within bacterial colonies grown on agar. The different microbial species and functional attributes produced striking differences in the morphology of precipitated crystals. The phylogenetic sequencing of 16S ribosomal RNA genes produced several isolates that are mostly related to the Bacillus group. One strain of promising results was selected and the environmental and nutritional conditions were characterized. The growth curve of the selected strain with an optimized condition was investigated.

Sorghum Root Flavonoid Chemistry, Cultivar, and Frost Stress Effects on Rhizosphere Bacteria and Fungi

Biotic stresses, including fungal infections, result in increased production of flavonoid compounds, including 3-deoxyanthocyanidins (3-DAs), in the leaf tissues of Sorghum bicolor. Our objectives were to determine whether sorghum genotypic variation influenced root flavonoid and 3-DA concentrations and rhizosphere microbial communities and to identify how these relationships were affected by abiotic stress. We evaluated root chemicals and rhizosphere microbiomes of five near-isogenic lines of sorghum before and after a late-season frost. Roots were analyzed for total flavonoids, total phenolics, 3-DA concentrations, and antioxidant activity. Amplicon sequencing of 16S ribosomal RNA genes and internal transcribed spacer regions was performed on rhizosphere soils. Concentrations of luteolinidin (a 3-DA) and total flavonoids differed between several lines before frost; however, these relationships changed after frost. Luteolinidin increased in three lines after frost, whereas total flavonoids decreased in all the lines after frost. Lines that differed in luteolinidin and total flavonoid concentrations before frost were different from those after frost. Rhizosphere community compositions also differed before and after frost but only fungal community compositions differed among sorghum lines. Bacterial community compositions were highly correlated with total flavonoid and luteolinidin concentrations. Furthermore, a greater number of bacterial taxa were correlated with total flavonoids and luteolinidin compared with fungal taxa. Collectively, this study provides evidence that plant genotypic variation influences root flavonoids and rhizosphere community composition and that these relationships are affected by frost. Plant–microbe interactions and secondary metabolite production may be important components to include for selective breeding of sorghum for frost stress tolerance.

Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease.

Emerging evidence suggests that the gut microbiome actively regulates cognitive functions and that gut microbiome imbalance is associated with Alzheimer's disease (AD), the most prevalent neurodegenerative disorder. However, the changes in gut microbiome composition in AD and their association with disease pathology, especially in the early stages, are unclear. Here, we compared the profiles of gut microbiota between APP/PS1 transgenic mice (an AD mouse model) and their wild-type littermates at different ages by amplicon-based sequencing of 16S ribosomal RNA genes. Microbiota composition started diverging between the APP/PS1 and wild-type mice at young ages (i.e., 1–3 months), before obvious amyloid deposition and plaque-localized microglial activation in the cerebral cortex in APP/PS1 mice. At later ages (i.e., 6 and 9 months), there were distinct changes in the abundance of inflammation-related bacterial taxa including Escherichia-Shigella, Desulfovibrio, Akkermansia, and Blautia in APP/PS1 mice. These findings suggest that gut microbiota alterations precede the development of key pathological features of AD, including amyloidosis and plaque-localized neuroinflammation. Thus, the investigation of gut microbiota might provide new avenues for developing diagnostic biomarkers and therapeutic targets for AD.

Vancomycin improves Plasmodium yoelii malaria parasite in vitro liver stage cultures by controlling Elizabethkingia anophelis, a bacterium in the microbiome of lab-reared Anopheles mosquitoes

Studies of Plasmodium sporozoites and liver stages require dissection of Anopheles mosquitoes to obtain sporozoites for experiments. Sporozoites from the rodent parasite P. yoelii are routinely used to infect hepatocytes for liver stage culture, but sometimes these cultures become contaminated. Using standard microbiological techniques, a single colony type of Gram-negative rod-shaped bacteria was isolated from contaminated cultures. Mass spectrometry and sequencing of the bacterial 16S ribosomal RNA gene identified the contaminant as Elizabethkingia spp. Based on sequence comparison and published studies of the Anopheles microbiome, the best match was E. anophelis. Culture contamination was not ameliorated by density gradient purification of sporozoites. However, the addition of vancomycin to the culture media consistently reduced contamination and improved culture outcomes as measured by liver stage parasite size. Thus, mosquito salivary gland-derived E. anophelis is identified a potential contaminant of Plasmodium liver stage cultures that can be mitigated by the addition of antibiotics.

Co-cultured non-marine ostracods from a temporary wetland harbor host-specific microbiota of different metabolic profiles

Rapid development of high-throughput sequencing methods and metagenomics revealed a diverse world of microbiota associated with multicellular organisms. Although recent discoveries indicate that freshwater invertebrates are hosts for specific bacteria, it is still unknown if this specificity is driven by host-derived factors or by the environment, especially in animals with diapause in ephemeral habitats, where parents and offspring are separated in time and space. In this work, using both low-throughput molecular approach and Next-generation sequencing of 16S ribosomal RNA gene, we present a taxonomic analysis of bacteria associated with two species of non-marine ostracods Sclerocypris tuberculata and Potamocypris mastigophora raised from diapausing eggs and co-cultured in laboratory conditions. Our analysis showed that despite sharing the same environment, each ostracod host developed distinct bacterial communities. The major difference was caused by the dominance of the family Comamonadaceae (Betaproteobacteria) in P. mastigophora and the Aeromonadaceae (Gammaproteobacteria) in S. tuberculata. Furthermore, prediction of metabolic pathways in metagenomes, revealed that microbiota of P. mastigophora exhibit higher number of sequences associated with the membrane transport and xenobiotics biodegradation and metabolism. Our study not only provides an insight into microbiota of non-marine ostracods but also shows that different ostracod species host functionally distinct bacterial communities.

Bacterial communities and nitrogen transformation genes in streambank legacy sediments and implications for biogeochemical processing

Streambank legacy sediments may be important sources of sediment and nutrients from Mid-Atlantic watersheds. However, little is known about the nutrient processing roles of microorganisms that inhabit legacy sediments, let alone their composition, diversity, and distributions. In this study, we sampled 15 streambanks at multiple depths throughout four watersheds in the Mid-Atlantic Region of the USA. High throughput sequencing of 16S ribosomal RNA genes indicated that streambank microbial community composition varied within site depth and across contemporary land uses. Collectively, the most abundant microbial taxa in legacy sediments included Acidobacteria (25–45%), Proteobacteria (15–40%), Nitrospirae (2–10%), Chloroflexi (1–5%), and Actinobacteria (1–10%). Bacterial community composition was distinct between agriculture and urban sites as well as suburban and urban sites. There was significant variation in community composition between the top (1–25%), upper-middle (26–50%), and bottom layers (76–100%) of sediments, while the relative abundances differed between layers for only Acidobacteria and Proteobacteria. Several streambank chemistry variables (metals, %TC, and %TN) had weak positive correlations with community composition. Compared to ammonia-oxidizing bacteria, nitrifying archaea were more predominant. This study provides the first insights into detailed microbial composition of legacy sediments and identifies environmental drivers for community structure and nitrogen processing. Future studies should consider exploring the role of this unique microbial environment for nutrient processing and leaching from legacy sediments and its implications for watershed water quality.

Host Plants Influence the Symbiont Diversity of Eriosomatinae (Hemiptera: Aphididae).

Eriosomatinae is a particular aphid group with typically heteroecious holocyclic life cycle, exhibiting strong primary host plant specialization and inducing galls on primary host plants. Aphids are frequently associated with bacterial symbionts, which can play fundamental roles in the ecology and evolution of their host aphids. However, the bacterial communities in Eriosomatinae are poorly known. In the present study, using high-throughput sequencing of the bacterial 16S ribosomal RNA gene, we surveyed the bacterial flora of eriosomatines and explored the associations between symbiont diversity and aphid relatedness, aphid host plant and geographical distribution. The microbiota of Eriosomatinae is dominated by the heritable primary endosymbiont Buchnera and several facultative symbionts. The primary endosymbiont Buchnera is expectedly the most abundant symbiont across all species. Six facultative symbionts were identified. Regiella was the most commonly identified facultative symbiont, and multiple infections of facultative symbionts were detected in the majority of the samples. Ordination analyses and statistical tests show that the symbiont community of aphids feeding on plants from the family Ulmaceae were distinguishable from aphids feeding on other host plants. Species in Eriosomatinae feeding on different plants are likely to carry different symbiont compositions. The symbiont distributions seem to be not related to taxonomic distance and geographical distance. Our findings suggest that host plants can affect symbiont maintenance, and will improve our understanding of the interactions between aphids, their symbionts and ecological conditions.