Human gut resistome can be country-specific
The emergence and spread of antibiotic resistance have become emerging threats to human health. The human gut is a large reservoir for antibiotic resistance genes. The gut resistome may be influenced by many factors, but the consumption of antibiotics at both individual and country level should be one of the most significant factors. Previous studies have suggested that the gut resistome of different populations may vary, but lack quantitative characterization supported with relatively large datasets. In this study, we filled the gap by analyzing a large gut resistome dataset of 1,267 human gut samples of America, China, Denmark, and Spain. We built a stacking machine-learning model to determine whether the gut resistome can act as the sole feature to identify the nationality of an individual reliably. It turned out that the machine learning method could successfully identify American, Chinese, Danish, and Spanish populations with F1 score of 0.964, 0.987, 0.971, and 0.986, respectively. Our finding does highlight the significant differences in the composition of the gut resistome among different nationalities. Our study should be valuable for policy-makers to look into the influences of country-specific factors of the human gut resistome.
Xia et al. (2019) Human gut resistome can be country-specific. PeerJ 7:e6389 https://doi.org/10.7717/peerj.6389
Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress
The red-eared slider (Trachemys scripta elegans), identified as one of the 100 most invasive species in the world, is a freshwater turtle originally from the eastern United States and northeastern Mexico. Field investigations have shown that T. s. elegans can survive and lay eggs in saline habitats. In order to understand the molecular mechanisms of salinity adaptation, high-throughput RNA-Seq was utilized to identify the changes in gene expression profiles in the liver of T. s. elegans in response to elevated salinity. We exposed individuals to 0, 5, or 15 psu (practical salinity units) for 30 days. A total of 157.21 million reads were obtained and assembled into 205138 unigenes with an average length of 620 bp and N50 of 964 bp. Of these, 1019 DEGs (differentially expressed genes) were found in the comparison of 0 vs. 5 psu, 1194 DEGs in 0 vs. 15 psu and 1180 DEGs in 5 vs. 15 psu, which are mainly related to macromolecule metabolic process, ion transport, oxidoreductase activity and generation of precursor metabolites and energy by GO (Gene Ontology) enrichment analyses. T. s. elegans can adapt itself into salinity by balancing the entry of sodium and chloride ions via the up-regulation expression genes of ion transport (potassium voltage-gated channel subfamily H member 5, KCNH5; erine/threonine-protein kinase 32, STK32; salt-inducible kinase 1, SIK1; adiponectin, ACDC), and by accumulating plasma urea and free amino acid via the up-regulation expression genes of amino acid metabolism (ornithine decarboxylase antizyme 3, OAZ3; glutamine synthetase, GLUL; asparaginase-like protein 1b, ASRGL; L-amino-acid oxidase-like, LAAO; sodium-dependent neutral amino acid transporter B, SLC6A15s; amino acid permease, SLC7A9) in response to osmotic regulation. An investment of energy to maintain their homeostatic balance is required to salinity adaptation, therefore, the genes related to energy production and conversion (F-ATPase protein 6, ATP6; cytochrome c oxidase subunit I, COX1; cytochrome c oxidase subunit III, COX3; cytochrome b, CYTb; cytochrome P450 17A1, CYP17A1) were up-regulated with the increase of gene expression associated with lipid metabolism (apolipoprotein E precursor, APoE; coenzyme Q-binding protein, CoQ10; high-density lipoprotein particle, SAA) and carbohydrate metabolism (HK, MIP). These findings improve our understanding of the underlying molecular mechanisms involved in salinity adaptation and provide general guidance to illuminate the invasion potential of T. s. elegans into saline environments.
Hong et al. (2019) Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress. PeerJ 7:e6538 https://doi.org/10.7717/peerj.6538
Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California
Background In this study cull dairy cows from six California dairy herds were sampled seasonally over the course of a year. The objectives were to determine the prevalence of antimicrobial resistant (AMR) Salmonella spp. shed in cull cow feces, and the factors associated with fecal shedding of AMR and multidrug resistant (MDR) Salmonella. Methods Six dairy farms located in the San Joaquin Valley of California were identified and enrolled as a convenience sample. On each dairy, and once during each of the four seasons, 10 cull cows were randomly selected for fecal sampling on the day of their removal from the herd. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous 4 month’s herd management and the specific cattle sampled. Fecal samples were submitted to the California Animal Health and Food Safety laboratory for Salmonella isolation. Antimicrobial resistance was evaluated using broth microdilution method and a gram-negative assay plate following Clinical Laboratory Standards Institute (CLSI) guidelines and breakpoint references. All statistical models were survey adjusted for number of animals on sampling day. Results A total of 62 Salmonella were isolated from 60 of the 239 fecal samples collected. For 12% (95% confidence interval (CI) [3–20]) of fecal samples a multidrug resistant Salmonella was isolated. The survey-weighted results for the two most common drug classes for which isolates were resistant were tetracycline (39%; 95% CI [27–51]) and ampicillin (18%; 95% CI [9–27]). An important finding was the identification of cephalosporin as the third most common drug class for which isolates were resistant, with ceftriaxone (10%; 95% CI [2–17]) being the most common drug associated with resistance in that class. At the cow-level, reason for culling, prior treatment with antimicrobial drugs as the reason for culling was associated with higher odds of isolating an AMR Salmonella isolate. At the herd-level, percent of animals monthly culled on the farm as well as number of milking cows in the herd were associated with isolation of antimicrobial resistant Salmonella in cull cows. Discussion Salmonella isolated from fecal samples from cull cows were resistant to important antimicrobials, such as ceftriaxone. The most common drug classes for which isolates were resistant were tetracyclines and beta-lactams, with ampicillin, ceftriaxone and ceftiofur being the three most common drugs within the latter. Cow and herd level factors were associated with isolating antimicrobial resistant Salmonella that should be further investigated for their potential role in promoting occurrence of AMR Salmonella. Our results also highlight the importance of monitoring dairy cattle sent to slaughter for shedding of Salmonella resistant to medically important antimicrobial drugs.
Pereira et al. (2019) Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California. PeerJ 7:e6546 https://doi.org/10.7717/peerj.6546
Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan
We report seven species of the genus Henricia Gray, 1840 that were found in Vostok Bay, and two species from adjacent area, known from museum collection or seen in underwater footage. while existing literature reported no confirmed species from this area. Most of these species: H. djakonovi, H. alexeyi, H. densispina, H. hayashii, H. granulifera, H. pacifica, H. asiatica, and H. oculata robusta were reported from the Sea of Japan previously. H. nipponica, known from Japan, is reported from Russian seas for the first time. All studied taxa are re-described here using a range of morphological characters and partial 16S rRNA nucleotide sequences, life colorations of several species are reported for the first time, and an identification key is provided. Lectotype designations are fixed for studied series of species described by AM Djakonov.
Chichvarkhin et al. (2019) Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan. PeerJ 7:e6585 https://doi.org/10.7717/peerj.6585
Spatial near future modeling of land use and land cover changes in the temperate forests of Mexico
The loss of temperate forests of Mexico has continued in recent decades despite wide recognition of their importance to maintaining biodiversity. This study analyzes land use/land cover change scenarios, using satellite images from the Landsat sensor. Images corresponded to the years 1990, 2005 and 2017. The scenarios were applied for the temperate forests with the aim of getting a better understanding of the patterns in land use/land cover changes. The Support Vector Machine (SVM) multispectral classification technique served to determine the land use/land cover types, which were validated through the Kappa Index. For the simulation of land use/land cover dynamics, a model developed in Dinamica-EGO was used, which uses stochastic models of Markov Chains, Cellular Automata and Weight of Evidences. For the study, a stationary, an optimistic and a pessimistic scenario were proposed. The projections based on the three scenarios were simulated for the year 2050. Five types of land use/land cover were identified and evaluated. They were primary forest, secondary forest, human settlements, areas without vegetation and water bodies. Results from the land use/land cover change analysis show a substantial gain for the secondary forest. The surface area of the primary forest was reduced from 55.8% in 1990 to 37.7% in 2017. Moreover, the three projected scenarios estimate further losses of the surface are for the primary forest, especially under the stationary and pessimistic scenarios. This highlights the importance and probably urgent implementation of conservation and protection measures to preserve these ecosystems and their services. Based on the accuracy obtained and on the models generated, results from these methodologies can serve as a decision tool to contribute to the sustainable management of the natural resources of a region.
Spatial and Geographic Information Science
Prieto-Amparán et al. (2019) Spatial near future modeling of land use and land cover changes in the temperate forests of Mexico. PeerJ 7:e6617 https://doi.org/10.7717/peerj.6617
Improvement of hydrogen production from Chlorella sp. biomass by acid-thermal pretreatment
Background Owing to the high growth rate, high protein and carbohydrate contents, and an ability to grow autotrophically, microalgal biomass is regarded as a promising feedstock for fermentative hydrogen production. However, the rigid cell wall of microalgae impedes efficient hydrolysis of the biomass, resulting in low availability of assimilable nutrients and, consequently, low hydrogen production. Therefore, pretreatment of the biomass is necessary in order to achieve higher hydrogen yield (HY). In the present study, acid-thermal pretreatment of Chlorella sp. biomass was investigated. Conditions for the pretreatment, as well as those for hydrogen production from the pretreated biomass, were optimized. Acid pretreatment was also conducted for comparison. Results Under optimum conditions (0.75% (v/v) H2SO4, 160 °C, 30 min, and 40 g-biomass/L), acid-thermal pretreatment yielded 151.8 mg-reducing-sugar/g-biomass. This was around 15 times that obtained from the acid pretreatment under optimum conditions (4% (v/v) H2SO4, 150 min, and 40 g-biomass/L). Fermentation of the acid-thermal pretreated biomass gave 1,079 mL-H2/L, with a HY of 54.0 mL-H2/g-volatile-solids (VS), while only 394 mL/L and 26.3 mL-H2/g-VS were obtained from the acid-pretreated biomass. Conclusions Acid-thermal pretreatment was effective in solubilizing the biomass of Chlorella sp. Heat exerted synergistic effect with acid to release nutrients from the biomass. Satisfactory HY obtained with the acid-thermal pretreated biomass demonstrates that this pretreatment method was effective, and that it should be implemented to achieve high HY.
Giang et al. (2019) Improvement of hydrogen production from Chlorella sp. biomass by acid-thermal pretreatment. PeerJ 7:e6637 https://doi.org/10.7717/peerj.6637
The chemical composition of a new “mica sandwich” foraminiferal species from the East Coast of Korea: Capsammina crassa sp. nov.
We describe a new agglutinated monothalamous foraminiferal species, Capsammina crassa sp. nov., based on integrated observations of the test morphology and the chemical characteristics of materials composing the test. The new species was found at a depth of <60 m on the East coast of Korea. The test morphology is typical of the genus Capsammina, comprising two or more mica plates with a ring of finely agglutinated mineral grains sandwiched between them and surrounding the cell body. There is no distinct test aperture. Elemental analyses of the agglutinated grains revealed 15 different types of mineral grains of which quartz is the most abundant. The surface areas of grains exposed on fractured surfaces ranged from 1.6 to 7,700 μm2 and the large plate-like grains forming the upper and lower surfaces measured about 420–2,350 μm in maximum width. The new species is morphologically similar to C. patelliformis, however, the differences in size, distribution area and depth support that these two species are distinct. This discovery is the first record of the genus Capsammina from the North Pacific. Therefore, it extends the biodiversity and geographical distribution of the genus Capsammina, which has been reported only from the bathyal NE Atlantic. Our finding also suggests the possibility of additional discovery of monothalamous foraminifera from around Korea.
Lee et al. (2019) The chemical composition of a new “mica sandwich” foraminiferal species from the East Coast of Korea: Capsammina crassa sp. nov.. PeerJ 7:e6642 https://doi.org/10.7717/peerj.6642
Dose-dependent and strain-dependent anti-obesity effects of Lactobacillus sakei in a diet induced obese murine model
Background Overweight and abdominal obesity, in addition to medical conditions such as high blood pressure, high blood sugar and triglyceride levels, are typical risk factors associated with metabolic syndrome. Yet, considering the complexity of factors and underlying mechanisms leading to these inflammatory conditions, a deeper understanding of this area is still lacking. Some probiotics have a reputation of a relatively-long history of safe use, and an increasing number of studies are confirming benefits including anti-obesity effects when administered in adequate amounts. Recent reports demonstrate that probiotic functions may widely differ with reference to either intra-species or inter-species related data. Such differences do not necessarily reflect or explain strain-specific functions of a probiotic, and thus require further assessment at the intra-species level. Various anti-obesity clinical trials with probiotics have shown discrepant results and require additional consolidated studies in order to clarify the correct dose of application for reliable and constant efficacy over a long period. Methods Three different strains of Lactobacillus sakei were administered in a high-fat diet induced obese murine model using three different doses, 1 × 1010, 1 × 109 and 1 × 108 CFUs, respectively, per day. Changes in body and organ weight were monitored, and serum chemistry analysis was performed for monitoring obesity associated biomarkers. Results Only one strain of L. sakei (CJLS03) induced a dose-dependent anti-obesity effect, while no correlation with either dose or body or adipose tissue weight loss could be detected for the other two L. sakei strains (L338 and L446). The body weight reduction primarily correlated with adipose tissue and obesity-associated serum biomarkers such as triglycerides and aspartate transaminase. Discussion This study shows intraspecies diversity of L. sakei and suggests that anti-obesity effects of probiotics may vary in a strain- and dose-specific manner.
Ji et al. (2019) Dose-dependent and strain-dependent anti-obesity effects of Lactobacillus sakei in a diet induced obese murine model. PeerJ 7:e6651 https://doi.org/10.7717/peerj.6651
Maintenance of dominant populations in heavily grazed grassland: Inference from a Stipa breviflora seed germination experiment
An understanding of population adaptation and maintenance mechanisms under interference from large herbivores is lacking and is a major focus of ecological research. In the Eurasian steppe, which has been subjected to continuous interference from domesticated ungulates throughout history and shows increased grazing, it is particularly urgent to analyze the ecological adaptation strategies of widely distributed Stipa plants. In this study, Stipa breviflora in a group of desert steppes in the Mongolian Plateau was selected to study the potential mechanism underlying the maintenance of dominant populations under the continuous interference of heavy grazing from the new perspective of seed germination rate. Laboratory experimental results showed that the values of the phenotypic traits of S. breviflora seeds were lower under a heavy grazing treatment than under a non-grazing treatment, but the seed germination rate did not decrease. The awns of non-grazed seeds significantly affected the seed germination rate, while those of heavily grazed seeds did not. Field observations showed that grazing does not significantly affect the population density of S. breviflora at different growth stages except in extremely wet and dry years. Our study suggests that under heavy grazing, S. breviflora uses an “opportunistic” ecological strategy to ensure population maintenance by increasing the seed germination rate and reducing dispersal via changes in associated seed phenotypic traits.
Liu et al. (2019) Maintenance of dominant populations in heavily grazed grassland: Inference from a Stipa breviflora seed germination experiment. PeerJ 7:e6654 https://doi.org/10.7717/peerj.6654
Minimum inhibitory concentration of nano-silver bactericides for beneficial microbes and its effect on Ralstonia solanacearum and seed germination of Japanese Cucumber (Cucumis sativus)
Background Plant growth-promoting rhizobacteria (PGPR) are highly promising biofertilizers that contribute to eco-friendly sustainable agriculture. There have been many reports on the anti-microbial properties of nanoparticles (NPs). Toxic effects of NPs under laboratory conditions have also reported; however, there is a lack of information about their uptake and mobility in organisms under environmental conditions. There is an urgent need to determine the highest concentration of NPs which is not detrimental for growth and proliferation of PGPR. Methods Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were used to measure the size and shape of NPs. Minimum inhibitory concentrations (MIC) of nano-silver on selected beneficial microbes and Ralstonia solanacearum were measured using the microdilution broth method. The percentage of seed germination was measured under in vitro conditions. Results NPs were spherical with a size of 16 ± 6 nm. Nano-silver at 12–40 mg l−1 inhibited the growth of bacteria. Seed application at 40 mg l−1 protected seeds from R. solanacearum and improved the rate of seed germination.
Sotoodehnia et al. (2019) Minimum inhibitory concentration of nano-silver bactericides for beneficial microbes and its effect on Ralstonia solanacearum and seed germination of Japanese Cucumber (Cucumis sativus). PeerJ 7:e6418 https://doi.org/10.7717/peerj.6418