Microbiome Profiling Using Shotgun Metagenomic Sequencing Identified Unique Microorganisms in COVID-19 Patients With Altered Gut Microbiota

COVID-19 is mainly associated with respiratory distress syndrome, but a subset of patients often present gastrointestinal (GI) symptoms. Imbalances of gut microbiota have been previously linked to respiratory virus infection. Understanding how the gut–lung axis affects the progression of COVID-19 can provide a novel framework for therapies and management. In this study, we examined the gut microbiota of patients with COVID-19 (n = 47) and compared it to healthy controls (n = 19). Using shotgun metagenomic sequencing, we have identified four microorganisms unique in COVID-19 patients, namely Streptococcus thermophilus, Bacteroides oleiciplenus, Fusobacterium ulcerans, and Prevotella bivia. The abundances of Bacteroides stercoris, B. vulgatus, B. massiliensis, Bifidobacterium longum, Streptococcus thermophilus, Lachnospiraceae bacterium 5163FAA, Prevotella bivia, Erysipelotrichaceae bacterium 6145, and Erysipelotrichaceae bacterium 2244A were enriched in COVID-19 patients, whereas the abundances of Clostridium nexile, Streptococcus salivarius, Coprococcus catus, Eubacterium hallii, Enterobacter aerogenes, and Adlercreutzia equolifaciens were decreased (p < 0.05). The relative abundance of butyrate-producing Roseburia inulinivorans is evidently depleted in COVID-19 patients, while the relative abundances of Paraprevotella sp. and the probiotic Streptococcus thermophilus were increased. We further identified 30 KEGG orthology (KO) modules overrepresented, with 7 increasing and 23 decreasing modules. Notably, 15 optimal microbial markers were identified using the random forest model to have strong diagnostic potential in distinguishing COVID-19. Based on Spearman’s correlation, eight species were associated with eight clinical indices. Moreover, the increased abundance of Bacteroidetes and decreased abundance of Firmicutes were also found across clinical types of COVID-19. Our findings suggest that the alterations of gut microbiota in patients with COVID-19 may influence disease severity. Our COVID-19 classifier, which was cross-regionally verified, provides a proof of concept that a set of microbial species markers can distinguish the presence of COVID-19.

Comparative Assessment of Physical and Chemical Characteristics of Prickly Pear Seed Oil from Opuntia ficus-indica and Opuntia megacantha Varieties

The prickly pear (Opuntia spp.) is an important plant in the economies of arid and semiarid areas, considering its low agronomic requirements and high water use efficiency. Characterizing the chemical composition of this plant will open new avenues for food, pharmaceutical, and cosmetic applications. In this context, this study examined the physical and chemical parameters of fruit seed oils of two prickly pear species from Rhamna area located in the center of Morocco: Opuntia ficus-indica (OFI), represented by the varieties “Safra” and “Aakria,” and Opuntia megacantha (OM), represented by the variety “Derbana.” The evaluated parameters included oil content, free acidity, specific extinction coefficients (K232 and K270), pigment content, fatty acid, and triglyceride composition. The seed oil contents of the three varieties “Safra,” “Aakria,” and “Derbana” were 8.09%, 8.74%, and 8.04%, respectively. OM (“Derbana”) seed oil was the most stable. The three studied varieties had higher contents of α-pheophytin and carotenoids than that of chlorophyll. Oil from the “Aakria” variety was distinguished by having the highest contents of α-pheophytin and chlorophyll. Significant differences in some fatty acid and triglyceride contents were noted. The major fatty acids of the three varieties were linoleic acid (60.55%–63.46%), followed by oleic acid (18.88%–21.81%) and palmitic acid (13.03%–13.75%). Furthermore, the chromatographic profiles of the triglycerides have shown the dominance of trilinolein (LLL, 24.33%–26.49%) and oleoyl-dilinoleoyl-glycerol (OLL, 20.92%–21.92%). Some triglycerides could be considered species markers, especially OLL, dipalmitoyl-linoleoyl-glycerol (PPL), oleoyl-linoleoyl-linolenoyl-glycerol and palmitoyl-oleoyl-dilinoleoyl-glycerol fraction (OLLn + PoLL), and stearoyl-dioleoyl-glycerol (SOO). This study provides a basis for qualitatively evaluating the therapeutic and cosmetic potential of prickly pear derivatives and for establishing quality standards of seed oil derived from the two species studied.

Biogenic Selenium Nanoparticles: Potential Solution to Oxidative Stress Mediated Inflammation in Rheumatoid Arthritis and Associated Complications

Rheumatoid arthritis (RA) is a common chronic inflammation-mediated disorder having systematic complications. RA triggers a self-directed inflammatory and immunological cascade that culminates in joint destruction. Though a range of treatment options are available, none of them are without adverse effects and this has led researchers to search for alternative solutions. Nanomedicine has emerged as a powerful therapeutic alternative, and selenium (Se) is an essential micronutrient trace element that has a crucial role in human health and disease. Selenium nanoparticles (SeNPs) derived from biological sources, such as plants, bacteria, fungi, and proteins, have exhibited remarkable candidate properties and toxicological profiles, and hence have shown potential to be used as antirheumatic agents. The potential of SeNPs can be attributed to the effect of functional groups bound to them, concentration, and most importantly to their nano range size. The antirheumatic effect of SeNPs is considerable due to its potential in amelioration of oxidative stress-mediated inflammation via downregulation of radical and nonradical species, markers of inflammation, and upregulation of inherent antioxidant defenses. The size and concentration impact of SeNPs has been shown in the subsequent antioxidant and anti-inflammatory properties. Moreover, the article emphasizes the role of these biogenic SeNPs as a notable option in the nanomedicine arena that needs to be further studied as a prospective remedial alternative to cure RA and medication-related adverse events.

Kidney resident macrophages in the rat have minimal turnover and replacement by blood monocytes

Kidney resident macrophages (KRM) are involved in maintaining renal homeostasis and in controlling the pathological outcome of acute kidney injury and cystic kidney disease in mice. In adult mice, KRM maintain their population through self-renewal with little or no input from the peripheral blood. Despite recent data suggesting that a transcriptionally similar population of KRM-like cells is present across species, the idea that they are self-renewing and independent of peripheral blood input in other species has yet to be proven due to the lack of an appropriate model and cross-species expression markers. In this study, we use our recently identified cross-species KRM cell surface markers and parabiosis surgery in inbred Lewis rats to determine if rat KRM are maintained independent of peripheral blood input, similar to their mouse counterparts. Flow cytometry analysis indicates that parabiosis surgery in the rat results in establishment of chimerism of T/B cells, neutrophils, and monocyte-derived infiltrating macrophages in the blood, spleen, and kidney three weeks post parabiosis surgery. Analysis of KRM using the cell surface markers CD81 or C1q indicates that these cells have minimal chimerism and, therefore, receive little input from the peripheral blood. Thus, a putative KRM population in the rat identified using two novel cross-species markers is maintained with minimal input from the peripheral blood confirming that KRM properties are conserved in at least two different species.

Genetic surveillance in the Greater Mekong Subregion and South Asia to support malaria control and elimination

ABSTRACTThe use of parasite genetic data by National Malaria Control Programmes (NMCPs) is currently limited, and typically focused on specific genetic features or a small number of study sites. We have developed GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion (GMS). By integrating simple sample collection procedures in the routine operations of public health facilities, GenRe-Mekong enables NMCPs to conduct large-scale surveillance project in endemic regions. Samples are processed by the SpotMalaria platform, which uses high-throughput technologies to produce a broad set of genotypes, including most known drug resistance markers, species markers and a genomic barcode. Through the application of heuristics based on published evidence, GenRe-Mekong delivers Genetic Report Cards, a compendium of genotypes and phenotype predictions that are used to map prevalence of resistance to multiple drugs. To date, GenRe-Mekong has worked with NMCPs in five countries, and with several large-scale research projects, processing 9,623 samples from clinical cases. The monitoring of resistance markers has been especially valuable for NMCPs tracking the recent rapid spread of DHA-piperaquine resistant parasites across the region. In Vietnam and Laos, data from GenRe-Mekong have provided novel knowledge about the spread of these resistant strains in provinces previously thought to be unaffected. GenRe-Mekong facilitates data sharing by aggregating at regional level results from different countries, providing cross-border views of the spread of resistant strains.

Distribution, Ecological and Phytocoenotical Features of Asparagus brachyphyllus Turcz. in Eastern Transbaicalia

Asparagus brachyphyllus Turcz. is a rare species in Russia. It’s a herbaceous perennial plant with short horizontal rhizome which gives 1-6 annual shoots. According to the literature the species grows in saline steppe and around salty lakes. In conditions of Eastern Transbaicalia vegetation lasts a little more than four months from middle May to late September, fruiting from June to September. A. brachyphyllus is listed in Red Book of Russian Federation, it is protected in Daursky State Nature Biosphere Reserve. In Transbaicalia it is limitated by small area of habitats, narrow environmental tolerance, low numerity of populations, grazing (annual shoots are eagerly eaten by animals, especially in spring). A. brachyphyllus has eastern-asian steppe (in the narrow sense) type of distribution, the main part of area is in North-East of China and in the East of Mongolia. In Russian Federation it occurs only in steppe districts of Zabaikalsky kray where there is the northern distribution limit. During our many years field expeditions new localities of A. brachyphyllus in Zabaikalsky Region were descripted, information on ecological-phytocenotic features and populations condition at the northern area limit was expanded. Localities of the species were identified at South and South-East of Zabaikalsky kray: Argun area, Aga steppe and Torey lake surroundings; most of localities are concentrated near Torey lakes, in other areas localities are sporadic. A. brachyphyllus grows mostly in Achnatherum splendens and Achnatherum splendens – Leymus chinensis saz steppe communities on solonetz soils, also on soil complexes of solonez and solonchack, sometimes it occurs on solonchacks in hyperhalophytic communities with Kalidium foliatum, Limonium aureum, Suaeda corniculata, Puccinellia tenuiflora. In plant communities A. brachyphyllus appears as a species with low abundance and coverage less 1%; due to prostrate form of shoots they place in lower layer up to 10 cm. In few-species communities on solonchacks A. brachyphyllus has low abundance, and a little higher on solonetz. In last case both species number and density of asparagus coenotic population are higher as usual. For estimation coenotic populations vitality we used a complex of criteria: density of coenotic populations, projective cover of species, markers of generativeness. Numerous Torey coenotic populations most often have medium vitality while that of coenotic populations at Aga localities higher. About a half of revealed coenotic populations suffer temperate influence of livestock grazing which lessens vitality by trampling and partial eating. Some localities at Torey lakes area need special protecting measures.

Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)

Background The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India. Results We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57–88%), polymorphism (3–9 alleles), heterozygosity (0.23–0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7 × 10−10 and 1.5 × 10−4, respectively, indicating a high statistical power in individual discrimination from poor quality samples. Conclusion Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore.

Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus): implications in population estimation and dynamics

BackgroundThe Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information and landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on field-collected dhole faeces in four tiger reserves of the central Indian landscape in the state of Maharashtra, India. Further, we conducted preliminary analyses of dhole population structure and demography in the study area.ResultsWe tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57-88%), polymorphism (3-9 alleles), heterozygosity (0.23-0.63) and produced a cumulative probability of identity (unbiased) and probability of identity (sibs) value of 4.7×10−10 and 1.5×10−4, respectively. Our preliminary analyses of population structure indicated four genetic subpopulations in dholes. Qualitative analyses of population demography show signal of population decline.ConclusionOur results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. Our methods can be used to estimate dhole populations and assess population trends for this elusive, social carnivore.