Gut Microbiota Reconstruction Following Host Infection with Bloodstage Plasmodium berghei ANKA Strain in a Murine Model

Malaria remains a global health problem.The relationship between Plasmodium spp.and the gut microbiota as well as the impact of Plasmodium spp.on the gut microbiota in vertebrate hosts is unclear.The aim of the current study was to evaluate the effect of blood-stage Plasmodium parasites on the gut microbiota of mice.The gut microbiota was analyzed by 16S rRNA sequencing and bioinformatic analyses at three stages.The gut microbiota changed during the three phases:the healthy stage,the infection stage,and the cure stage(on the 9th day after malarial elimination).Moreover,the gut microbiota of these infected animals did not recover after malaria infection.There were 254 operational taxonomic units(OTUs)across all three stages,and there were unique strains or OTUs at each stage of the experiment.The percentages of community abundance of 8 OTUs changed significantly(P<0.05).The dominant OTU in both the healthy mice and the mice with malaria was OTU265,while that in the cured mice was OTU234.In addition,the changes in OTU147 were the most noteworthy.Its percentage of community abundance varied greatly,with higher values during malaria than before malaria infection and after malaria elimination.These results indicated that the external environment influenced the gut microbiota after host C57BL/6 mice were infected with blood-stage P.berghei ANKA and that the same was true during and after elimination of blood-stage P.berghei ANKA.In addition,we could not isolate OTU147 for further study.This study identified gut microbiota components that were reconstructed after infection by and elimination of blood-stage P.berghei ANKA in host C57BL/6 mice,and this process was affected by P.berghei ANKA and the external environment of the host.

Structural and functional characteristics of microbiota in oropharynx of sub-healthy children with gastrointestinal heat retention syndrome differentiated by traditional Chinese medicine

Objective:To explore the structural and functional characteristics of microbiota in oropharynx of subhealthy children with gastrointestinal heat retention syndrome(GHRS)differentiated by traditional Chinese medicine,and screen the biometric operational taxonomic units(OTUs)to assist the clinical diagnosis.Methods:We recruited children according to the“GHRS diagnostic scale”,collected their oropharyngeal swabs,and sequenced the 16 SrDNA V4 region.We described the bacterial structure with alpha-indexes,beta-distances,and relative abundances;moreover,we screened the differential genera/OTUs with Wilcoxon rank-sum test,Metagenome Seq analysis,and linear discriminant analysis effect size(LEf Se)analysis,in which biometric OTUs were selected to construct the receiver operating characteristic curve to verify the diagnostic value.The bacterial function was predicted with Kyoto Encyclopedia of Genes and Genomes pathways according to 16S rDNA gene by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.Results:The study population was composed of 10 children with GHRS and 10 healthy control children.GHRS children were more likely to overeat(gluttony,P=.033).Alpha-indexes,such as Sobs,abundancebased coverage estimator,Bootstrap,and Qstat,were significantly higher in the GHRS group,while betadistances did not exhibit any significant intergroup differences.There were 9 differently distributed nonpredominant genera between the groups in Wilcoxon rank-sum test,as well as 13 non-predominant genera in Metagenome Seq analysis and 3 non-predominant OTUs in LEfSe analysis.OTU44 and OTU196 were used to construct the receiver operating characteristic curve,and the area under curve was 0.92.Predicted functions showed that pathways related to oxidative phosphorylation and carbon metabolism were enriched in healthy control samples,while the pathway related to renin secretion was remarkably enriched in GHRS samples.Conclusion:Unique oropharyngeal microbial structure and function were identified in GHRS children.OTU44 and OTU196 were specific OTUs,which could be used as biomarkers of GHRS to assist clinical diagnosis.

Insights into the divergent evolution of the oceanic squid Sthenoteuthis oualaniensis(Cephalopoda:Ommastrephidae)from the Indian Ocean

Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms(viz.middle-sized,dwarf,and giant forms)whose taxonomic status has been disputed for decades.This integrated taxonomic study examines these prevenient morphotypes gathered on cruises in the Indian Ocean to ascertain their status in the evolutionary history of the species.Molecular analyses employing mitochondrial(COI,ND2)and nuclear(H3)markers revealed four genetically distinct and novel lineages of the species in the Indian Ocean,representing three morphotypes from the Arabian Sea and one from the Southern Indian Ocean.The mitochondrial-based phylograms revealed two distinct clades in the species:“dwarf forms+giant form”and“middle-sized forms,”which further branch into geographically structured evolutionary units.Species delimitation analyses recovered five distinct clades,namely,the Arabian Sea giant and dwarf forms,Equatorial,Eastern Typical,and Other Middle-sized forms,representing the consensus molecular operational taxonomic units.H3 being heterozygous could not resolve the phylogeny.Haplotype network and AMOVA analysis of mtDNA genes indicated explicit phylogeographic structuring of haplotypes,whereas these outputs and PCA results were incongruent with the morphological grouping.Phenetic features distinguishing the morphotypes were sometimes plastic and mismatched with the genotypes.The giant form was genetically close to the dwarf forms,contradicting the earlier notion that it descended from the middle-sized form.It may be assumed that the dwarf form evolved following sympatric speciation and adaptation to warm equatorial waters,while the focal features of the Western Arabian Sea guide toward allopatric speciation of the giant form.

Abiotic and biotic drivers of struvite solubilization in contrasting soils

Phosphorus(P) limitation in the coming decades calls for the utilization of alternative fertilizers in agriculture. Struvite is a promising P source, but its potential role as a fertilizer is dependent on different physical, chemical, and biological properties, which are very heterogeneous in soil, complicating the prediction of the best soil conditions for its application. Here, we evaluated the solubility of struvite in soil, its redistribution into P fractions, and its potential abiotic and biotic drivers in 62 globally distributed soils with contrasting properties through an incubation assay. We found that after 40 d, about 35% of struvite P was redistributed into soil fractions more accessible to plants and microbes. Phosphorus redistribution from struvite was driven by a complex suite of soil physical, chemical, and microbial properties as well as environmental factors that varied across soils. Soil texture played a critical role in determining the redistribution of P in struvite-amended soils in soluble(H2O extraction), labile(NaHCO3 extraction), and moderately labile(NaOH extraction) fractions.In addition, the soil solution cation concentration was one of the most important drivers of available struvite-derived P fractions. The great importance of texture and cations in determining struvite-derived P fractions in soil was contrasted with the relatively minor role of pH. At the microbial level, the number of bacterial operational taxonomic units(OTUs) from the unfertilized soils that correlated with struvite-derived P fractions was higher than that of fungi. The number of OTUs that correlated with the struvite-derived soluble P fraction was dominated by fungi, whereas the number of OTUs that correlated with the struvite-derived labile P fraction was dominated by bacteria. Overall, this study provided a predictive framework for the potential use of struvite as a P fertilizer in contrasting soils.

Environmental similarity is more important than distance in the community structuring processes of ammonia-oxidizing archaea in agricultural soils

Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has poorly been understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate the beta nearest taxon index to quantify the influence of stochastic and deterministic processes. We found that spatial distance between samples predicted the perceived processes involved in community structuring, with stochastic processes dominating at local scales. At greater distances, stochasticity became weaker. However, soil pH, which was also the strongest determinant of AOA community, was a much stronger predictor of community structuring, leaving the distance effect redundant as an explanation of community structuring processes. The communities of AOA differing by less than 1 pH unit differed mainly stochastically in terms of operational taxonomic unit composition. At larger pH differences, deterministic processes based on heterogeneous selection between clades became increasingly dominant. It appears that AOA community composition is largely determined by the environment. However, very similar pH environments are the exception. In environments with very close pH values, stochastic effects dominantly cause differences in community composition, whether spatially near or far.

Metagenomic Surveys of Gut Microbiota

Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational tax- onomic unit （OTU） levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ulti- mately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interac- tion among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe-microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe-microbe inter- action networks.

Bacterial communities in paddy soils changed by milk vetch as green manure: A study conducted across six provinces in South China

The use of green manures contributes to sustainable soil and nutrient management in agriculture;however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncertain. A study was undertaken across multiple sites and years in Hunan, Jiangxi, Anhui, Henan,Hubei, and Fujian provinces of South China to investigate the effects of green manuring on the structure and function of soil bacterial communities in rice-green manure cropping systems. The study included four treatments: winter fallow with no chemical fertilizer as a control(NF), milk vetch as green manure without chemical fertilizer(GM), winter fallow and chemical fertilizer(CF), and a combination of chemical fertilizer and milk vetch(GMCF).Significant differences were found in the responses of soil microbial communities at different sites, with sampling sites explaining 72.33%(F = 36.59,P = 0.001) of the community composition variation. The bacterial communities in the soils from Anhui, Henan, and Hubei were broadly similar, while those from Hunan were distinctly different from other locations. The analysis of Weighted UniFrac distances showed that milk vetch changed soil microbial communities compared with winter fallow. Proteobacteria and Chloroflexi predominated in these paddy soils;however, the application of green manures increased the relative abundance of Actinobacteria. There was evidence showing that the functional microbes which play important roles in the cycling of soil carbon, nitrogen(N), and sulfur(S) changed after several years of milk vetch utilization(linear discriminant analysis score > 2). The abundance of methane-oxidizing bacteria and S-reducing bacteria increased, and microbes involved in N fixation, nitrification, and denitrification also increased in some provinces. We concluded that the application of milk vetch changed the bacterial community structure and affected the functional groups related to nutrient transformation in soils at a regional scale.

Exploring the interaction patterns among taxa and environments from marine metagenomic data

The sequencing revolution driven by high-throughput technologies has generated a huge amount of marine microbial sequences which hide the interaction patterns among microbial species and environment factors. Exploring these patterns is helpful for exploiting the marine resources. In this paper, we use the complex network approach to mine and analyze the interaction patterns of marine taxa and environments in spring, summer, fall and winter seasons. With the 16S rRNA pyrosequencing data of 76 time point taken monthly over 6 years, we first use our MtHc clustering algorithm to generate the operational taxonomic units （OTUs）. Then, employ the k-means method to divide 76 time point samples into four seasonal groups, and utilize mutual information （MI） to construct the four correlation networks among microbial species and environment factors. Finally, we adopt the symmetrical non-negative matrix factorization method to detect the interaction patterns, and analysis the relationship between marine species and environment factors. The results show that the four seasonal microbial interaction networks have the characters of complex networks, and interaction patterns are related with the seasonal variability; the same environmental factor influences different species in the four seasons; the four environmental factors of day length, photosynthetically active radiation, NO2＋ NO3 and silicate may have stronger influences on microbes than other environment factors.

Bacterial communities associated with natural and commercially grown rooibos (Aspalathus linearis)

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea.Symbiotic interactions between A.linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor,acidic fynbos soil.The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A.linearis,as well as the effect of seasonal changes on these communities.Bacterial communities were characterized using high throughput amplicon sequencing,and their correlations with soil chemical properties were investigated.The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction.Actinobacteria,Proteobacteria,and Acidobacteria were the most dominant bacterial phyla detected in this study.Highly similar bacterial communities were associated with natural and commercially grown plants.Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season,while no significant differences were detected in the wet season.This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A.linearis.