Results Of Microbiome Analyses Research Articles

Ecological and evolutionary inferences from aphid microbiome analyses depend on methods and experimental design

AbstractIntroductionAphids play an important role in agroecological contexts as pests and vectors of plant diseases. Aphid performance is closely connected to microbial endosymbionts that provide different benefits or costs to both the aphids and their hosts plants. Furthermore, the microbiome of aphids is connected to soil microbiomes via the plant. Aphid microbiome experiments usually include a pooling step, where several individuals are sequenced together to obtain sufficient DNA concentrations but pooling may blur intraspecific variations.Materials and MethodsTo investigate the effects of sequencing single versus pooled aphids on the results of microbiome analyses, we compared 16S rRNA/ITS amplicon libraries from pooled and single oak aphids (Tuberculatus annulatus HARTIG) under three different soil treatments. We tested whether results quantitatively or qualitatively depend on pooling aphids, prevalence‐based in silico filtering or removal of the primary endosymbiont (Buchnera aphidicola). Buchnera phylogeny, prevalence and abundance of secondary endosymbionts and effects of soil microbiota were investigated.ResultsPooling leads to quantitative differences in bacteria and qualitative differences in fungal species richness, bacterial community composition and partially fungal community composition. Filtering‐dependent results were obtained for bacterial evenness. Buchnera phylogeny supports the hypothesis of cospeciation of primary endosymbionts in oak aphids. We detected Arsenophonus, Hamiltonella, Rickettsia, Rickettsiella, Serratia and Sphingopyxis in oak aphids, with their prevalence and abundance partially affected by pooling. Pooling leads to overestimating the frequency of multispecies endosymbiont infections, while underestimating their relative abundance.ConclusionWe hereby extend our view on non‐model aphid microbiomes and identify pitfalls in experimental design in aphid microbiome research.

Microbial community dynamics during anaerobic co-digestion of corn stover and swine manure at different solid content, carbon to nitrogen ratio and effluent volumetric percentages

The methane production and the microbial community dynamics of thermophilic anaerobic co-digestion (AD) of corn stover, swine manure and effluent were conducted at total solid (TS) content of 5%, 10% and 15%, the carbon to nitrogen ratio (C/N) of 20, 30 and 40 and the effluent volumetric percentage (EVP) of 20%, 40% and 60%. For batches with 5% TS, the highest methane yield of 238.5–283.1 mL g−1 volatile solid (VS) and the specific methane productivity of 138.5–152.2 mL g−1 initial VS were obtained at the C/N ratios of 20 and 30. For the mixtures with 10% and 15% TS, the highest methane yield was 341.9 mL g−1 VS and 351.2 mL g−1 VS, respectively, when the C/N ratio of 20% and 60% EVP conditions were maintained. Co-digestion of swine manure with corn stover caused an obvious shift in microbial population, in which the archaeal population changed from 0.3% to 2.8% and the bacterial community changed from 97.2% to 99.7%. The experimental batches with the highest relative abundance of the archaeal population (2.00% of total microbial population for 5% TS, 1.74% for 10% TS and 2.76% for 15% TS) had the highest rate of methanogenesis subsequently enhancing methane production (283.08 mL g−1 VS for 5% TS, 341.91 mL g−1 VS for 10% TS and 351.23 mL g−1 VS for 15% TS). The results of microbiome analysis enabled understanding the key populations in biomethane generation.

Microbiome and Culture Based Analysis of Chronic Rhinosinusitis Compared to Healthy Sinus Mucosa.

The role of bacteria in chronic rhinosinusitis (CRS) is still not well understood. Whole microbiome analysis adds new aspects to our current understanding that is mainly based on isolated bacteria. It is still unclear how the results of microbiome analysis and the classical culture based approaches interrelate. To address this, middle meatus swabs and tissue samples were obtained during sinus surgery in 5 patients with CRS with nasal polyps (CRSwNP), 5 patients with diffuse CRS without nasal polyps (CRSsNP), 5 patients with unilateral purulent maxillary CRS (upm CRS) and 3 patients with healthy sinus mucosa. Swabs were cultured, and associated bacteria were identified. Additionally, parts of each tissue sample also underwent culture approaches, and in parallel DNA was extracted for 16S rRNA gene amplicon-based microbiome analysis. From tissue samples 4.2 ± 1.2 distinct species per patient were cultured, from swabs 5.4 ± 1.6. The most frequently cultured species from the swabs were Propionibacterium acnes, Staphylococcus epidermidis, Corynebacterium spp. and Staphylococcus aureus. The 16S-RNA gene analysis revealed no clear differentiation of the bacterial community of healthy compared to CRS samples of unilateral purulent maxillary CRS and CRSwNP. However, the bacterial community of CRSsNP differed significantly from the healthy controls. In the CRSsNP samples Flavobacterium, Pseudomonas, Pedobacter, Porphyromonas, Stenotrophomonas, and Brevundimonas were significantly enriched compared to the healthy controls. Species isolated from culture did not generally correspond with the most abundant genera in microbiome analysis. Only Fusobacteria, Parvimonas, and Prevotella found in 2 unilateral purulent maxillary CRS samples by the cultivation dependent approach were also found in the cultivation independent approach in high abundance, suggesting a classic infectious pathogenesis of odontogenic origin in these two specific cases. Alterations of the bacterial community might be a more crucial factor for the development of CRSsNP compared to CRSwNP. Further studies are needed to investigate the relation between bacterial community characteristics and the development of CRSsNP.

Is human DNA enough?—potential for bacterial DNA

Is human DNA enough?—potential for bacterial DNA