Different analysis strategies of 16S rRNA gene data from rodent studies generate contrasting views of gut bacterial communities associated with diet, health and obesity
Background One of the main functions of diet is to nurture the gut microbiota and this relationship affects the health of the host. However, different analysis strategies can generate different views on the relative abundance of each microbial taxon, which can affect our conclusions about the significance of diet to gut health in lean and obese subjects. Here we explored the impact of using different analysis strategies to study the gut microbiota in a context of diet, health and obesity. Methods Over 15 million 16S rRNA gene sequences from published studies involving dietary interventions in obese laboratory rodents were analyzed. Three strategies were used to assign the 16S sequences to Operational Taxonomic Units (OTUs) based on the GreenGenes reference OTU sequence files clustered at 97% and 99% similarity. Results Different strategies to select OTUs influenced the relative abundance of all bacterial taxa, but the magnitude of this phenomenon showed a strong study effect. Different taxa showed up to 20% difference in relative abundance within the same study, depending on the analysis strategy. Very few OTUs were shared among the samples. ANOSIM test on unweighted UniFrac distances showed that study, sequencing technique, animal model, and dietary treatment (in that order) were the most important factors explaining the differences in bacterial communities. Except for obesity status, the contribution of diet and other factors to explain the variability in bacterial communities was lower when using weighted UniFrac distances. Predicted functional profile and high-level phenotypes of the microbiota showed that each study was associated with unique features and patterns. Conclusions The results confirm previous findings showing a strong study effect on gut microbial composition and raise concerns about the impact of analysis strategies on the membership and composition of the gut microbiota. This study may be helpful to guide future research aiming to investigate the relationship between diet, health, and the gut microbiota.
Garcia-Mazcorro et al. (2020) Different analysis strategies of 16S rRNA gene data from rodent studies generate contrasting views of gut bacterial communities associated with diet, health and obesity. PeerJ 8:e10372 https://doi.org/10.7717/peerj.10372
Investigation of acute-phase proteins and cytokines response in goats with contagious caprine pleuropneumonia with special reference to their diagnostic accuracy
Acute-phase proteins (APPs) have always had valued diagnostic potentialities in response to infection. This study aimed to evaluate the diagnostic accuracy of selected APPs and proinflammatory cytokines (PIC) in goats with contagious caprine pleuropneumonia (CCPP) under field conditions. Moreover, to highlight the role of tested biomarkers in CCPP pathogenesis. Fifty-eight goats (38 confirmed cases with CCPP and 20 healthy controls) were involved in this investigation. C-reactive protein (CRP), procalcitonin (PCT), haptoglobin (HP), fibrinogen (Fb), serum amyloid A (SAA), selected PIC (IL1-α, IL1-β, IL-6, interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α)) levels were investigated in serum samples from all goats under investigation. Latex agglutination test was used for diagnosis of goats with CCPP. For microbiological investigations, nasopharyngeal swabs (from all goats), lung tissues and pleural fluids (from only necropsied goats) were collected. This study revealed that all tested parameters have a high to moderate degree of diagnostic performance for CCPP. Magnitudes of increase in levels of APPs (CRP, HP and SAA) were stronger than PIC, IFN-γ, Fb and PCT. All tested parameters showed high diagnostic accuracy (AUROC >90%), except HP (AUROC = 87.3%) and IFN-γ (AUROC = 78.8%) showed moderate accuracy in differentiation of goats with and without CCPP infection. For detecting goats with and without CCPP infection, HP had the lowest sensitivity (Se = 81.6%) and Fb had the lowest specificity (Sp = 85.0%) among the APPs parameters tested. However, PCT showed the highest Se (100%) and Sp (95.0%) to detect goats with and without CCPP infection among tested parameters. Conclusively, this study endorses the significance of selected APPs and PIC as additional screening diagnostic parameters for naturally occurring CCPP in goats. However, it does not replace traditional methods for diagnosis of CCPP in goats. Furthermore, APPs and PIC have an important role in disease pathogenesis in goats.
El-Deeb et al. (2020) Investigation of acute-phase proteins and cytokines response in goats with contagious caprine pleuropneumonia with special reference to their diagnostic accuracy. PeerJ 8:e10394 https://doi.org/10.7717/peerj.10394
The easternmost occurrence of Mammut pacificus (Proboscidea: Mammutidae), based on a partial skull from eastern Montana, USA
Mammut pacificus is a recently described species of mastodon from the Pleistocene of California and Idaho. We report the easternmost occurrence of this taxon based upon the palate with right and left M3 of an adult male from the Irvingtonian of eastern Montana. The undamaged right M3 exhibits the extreme narrowness that characterizes M. pacificus rather than M. americanum. The Montana specimen dates to an interglacial interval between pre-Illinoian and Illinoian glaciation, perhaps indicating that M. pacificus was extirpated in the region due to habitat shifts associated with glacial encroachment.
McDonald et al. (2020) The easternmost occurrence of Mammut pacificus (Proboscidea: Mammutidae), based on a partial skull from eastern Montana, USA. PeerJ 8:e10030 https://doi.org/10.7717/peerj.10030
Acetate correlates with disability and immune response in multiple sclerosis
Background Gut microbiota has been related to multiple sclerosis (MS) etiopathogenesis. Short-chain fatty acids (SCFA) are compounds derived from microbial metabolism that have a role in gut-brain axis. Objectives To analyse SCFA levels in plasma of MS patients and healthy donors (HD), and the possible link between these levels and both clinical data and immune cell populations. Methods Ninety-five MS patients and 54 HD were recruited. Patients were selected according to their score in the Expanded Disability Status Scale (EDSS) (49 EDSS ≤ 1.5, 46 EDSS ≥ 5.0). SCFA were studied in plasma samples by liquid chromatography-mass spectrometry. Peripheral blood mononuclear cells were studied by flow cytometry. Gender, age, treatments, EDSS and Multiple Sclerosis Severity Score (MSSS) were evaluated at the recruitment. Results Plasma acetate levels were higher in patients than in HD (p = 0.003). Patients with EDSS ≥ 5.0 had higher acetate levels than those with EDSS≤ 1.5 (p = 0.029), and HD (p = 2.97e–4). Acetate levels correlated with EDSS (r = 0.387; p = 1.08e–4) and MSSS (r = 0.265; p = 0.011). In untreated MS patients, acetate levels correlated inversely with CD4+ naïve T cells (r = − 0.550, p = 0.001) and directly with CD8+ IL-17+ cells (r = 0.557; p = 0.001). Conclusions Plasma acetate levels are higher in MS patients than in HD. In MS there exists a correlation between plasma acetate levels, EDSS and increased IL-17+ T cells. Future studies will elucidate the role of SCFA in the disease.
Pérez-Pérez et al. (2020) Acetate correlates with disability and immune response in multiple sclerosis. PeerJ 8:e10220 https://doi.org/10.7717/peerj.10220
Diversity of edible insects in a Natural World Heritage Site of India: entomophagy attitudes and implications for food security in the region
Insects not only play a significant role in the ecological process of nature but since pre-historic times have also formed a part of the human diet. With a still growing population and skewed demographic structures across most societies of the world, their role as nutrient-rich food has been increasingly advocated by researchers and policymakers globally. In this study, we examine the edible insect diversity and entomophagy attitudes of ethnic people in Manas National Park, a UNESCO Natural World Heritage Site, located in Assam (India). The study involved a field investigation through which the pattern of entomophagy and the attitude towards insect-eating was studied. Following this, we examined the edible insect diversity and abundance at different sampling points. A total of 22 species of edible insects belonging to fifteen families and eight orders were recorded from different habitat types. Out of these 22 species, Orthopterans showed a maximum number of eight species followed by Hymenoptera (four), Hemiptera (three), Lepidoptera (two), Blattodea (two) and one species each from Coleoptera, Odonata, and Mantodea. Dominance, diversity, and equitability indices were computed along with the relative abundance of the insects concerning four habitat types. Aspects of the economic significance of entomophagy were also observed during the field investigation. To manage insects in the interest of food security, more attention should be given to sustainable collecting and rearing methods emphasizing their economic, nutritional, and ecological advantages.
Das et al. (2020) Diversity of edible insects in a Natural World Heritage Site of India: entomophagy attitudes and implications for food security in the region. PeerJ 8:e10248 https://doi.org/10.7717/peerj.10248
Nitrogen fertilization affects maize grain yield through regulating nitrogen uptake, radiation and water use efficiency, photosynthesis and root distribution
High external nitrogen (N) inputs can maximize maize yield but can cause a subsequent reduction in N use efficiency (NUE). Thus, it is necessary to identify the minimum effective N fertilizer input that does not affect maize grain yield (GY) and to investigate the photosynthetic and root system consequences of this optimal dose. We conducted a 4-year field experiment from 2014 to 2017 with four N application rates: 300 (N300), 225 (N225), 150 (N150), and 0 Kg ha−1 (N0) in the Northwest of China. GY was assessed by measuring the photosynthetic capacity and root system (root volume, surface area, length density and distribution). Grain yield decreased by −3%, 7.7%, and 21.9% when the N application rates decreased by 25%, 50%, and 100% from 300 Kg ha−1. We found that yield reduction driven by N reduction was primarily due to decreased radiation use efficiency (RUE) and WUE instead of intercepted photosynthetically active radiation and evapotranspiration. In the N225 treatment, GY, WUE, and RUE were not significantly reduced, or in some cases, were greater than those of the N300 treatment. This pattern was also observed with relevant photosynthetic and root attributes (i.e., high net photosynthetic rate, stomatal conductance, and root weight, as well as deep root distribution). Our results suggest that application of N at 225 Kg ha−1 can increased yield by improving the RUE, WUE, and NUE in semi-arid regions.
Su et al. (2020) Nitrogen fertilization affects maize grain yield through regulating nitrogen uptake, radiation and water use efficiency, photosynthesis and root distribution. PeerJ 8:e10291 https://doi.org/10.7717/peerj.10291
Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes
Background Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes. Methods A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms. Results Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).
Cheawchanlertfa et al. (2020) Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes. PeerJ 8:e10343 https://doi.org/10.7717/peerj.10343
Effects of microhabitat on rodent-mediated seed removal of endangered Kmeria septentrionalis in the karst habitat
Seed removal behaviors of rodents are largely influenced by microhabitat. Although the karst ecosystem is composed of a broad variety of microhabitats, we have no information on how they affect such behaviors. We investigated rodents’ seed removal behaviors in four karst microhabitats (stone cavern, stone groove, stone surface, and soil surface) using three types of Kmeria septentrionalis seeds: fresh, black (intact seeds with black aril that dehydrates and darkens), and exposed (clean seeds without the aril). We show that Rattus norvegicus, Leopoldamys edwardsi and Rattus flavipectus were the predominant seed predators. Even though all seed types experienced a high removal rate in all four microhabitats, but rodents preferentially removed seeds from the three stone microhabitats (stone caves: 69.71 ± 2.74%; stone surface: 60.53 ± 2.90%; stone groove: 56.94 ± 2.91%) compared to the soil surface (53.90 ± 2.92%). Seeds that had been altered by being exposed to the environment were more attractive to rodents than fresh seeds (76.25 ± 2.20% versus 36.18 ± 2.29%). The seed removal behavior of rodents was significantly affected by the microhabitat and seed type. Finally, seeds that had fallen on the soil surface microhabitat incurred a lower predation risk than seeds fallen on other microhabitats, which increased their probability to germinate. Our results indicate that the lower predation rate of seeds from the endangered K. septentrionalis dropped on the soil surface increases trees’ likelihood of survival.
Wang et al. (2020) Effects of microhabitat on rodent-mediated seed removal of endangered Kmeria septentrionalis in the karst habitat. PeerJ 8:e10378 https://doi.org/10.7717/peerj.10378
Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation
Background Human embryonic stem cells (hESC) have been an invaluable research tool to study motor neuron development and disorders. However, transcriptional regulation of multiple temporal stages from ESCs to spinal motor neurons (MNs) has not yet been fully elucidated. Thus, the goals of this study were to profile the time-course expression patterns of lncRNAs during MN differentiation of ESCs and to clarify the potential mechanisms of the lncRNAs that are related to MN differentiation. Methods We utilized our previous protocol which can harvest motor neuron in more than 90% purity from hESCs. Then, differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) during MN differentiation were identified through RNA sequencing. Bioinformatic analyses were performed to assess potential biological functions of genes. We also performed qRT-PCR to validate the DElncRNAs and DEmRNAs. Results A total of 441 lncRNAs and 1,068 mRNAs at day 6, 443 and 1,175 at day 12, and 338 lncRNAs and 68 mRNAs at day 18 were differentially expressed compared with day 0. Bioinformatic analyses identified that several key regulatory genes including POU5F1, TDGF1, SOX17, LEFTY2 and ZSCAN10, which involved in the regulation of embryonic development. We also predicted 283 target genes of DElncRNAs, in which 6 mRNAs were differentially expressed. Significant fold changes in lncRNAs (NCAM1-AS) and mRNAs (HOXA3) were confirmed by qRT-PCR. Then, through predicted overlapped miRNA verification, we constructed a lncRNA NCAM1-AS-miRNA-HOXA3 network.
Sun et al. (2020) Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation. PeerJ 8:e10075 https://doi.org/10.7717/peerj.10075
Regional infectious risk prediction of COVID-19 based on geo-spatial data
After the first confirmed case of the novel coronavirus disease (COVID-19) was found, it is of considerable significance to divide the risk levels of various provinces or provincial municipalities in Mainland China and predict the spatial distribution characteristics of infectious diseases. In this paper, we predict the epidemic risk of each province based on geographical proximity information, spatial inverse distance information, economic distance and Baidu migration index. A simulation study revealed that the information based on geographical economy matrix and migration index could well predict the spatial spread of the epidemic. The results reveal that the accuracy rate of the prediction is over 87.10% with a rank difference of 3.1. The results based on prior information will guide government agencies and medical and health institutions to implement responses to major public health emergencies when facing the epidemic situation.
Cheng et al. (2020) Regional infectious risk prediction of COVID-19 based on geo-spatial data. PeerJ 8:e10139 https://doi.org/10.7717/peerj.10139