Multiplex PCR reveals unique trends in pathogen and parasitoid infestations of alfalfa leafcutting brood cells.

The alfalfa leafcutting bee Megachile rotundata Fabricius (HYMENOPTERA: Megachilidae) is an important pollinator for multiple agricultural seed commodities in the United States. Megachile rotundata is a solitary bee that forms brood cocoons where its larvae can develop. During the developmental stages of growth, broods can be preyed upon by multiple different fungal and bacterial pathogens and insect predators and parasitoids, resulting in the loss of the developing larvae. Larval loss is a major concern for alfalfa (Medicago sativa L.) seed producers because they rely on pollinator services provided by Megachile rotundata and reduced pollination rates result in lower yields and increased production costs. In the present study, we examined the taxonomic composition of organisms found within M. rotundata brood cells using a multiplex PCR assay which was developed for the detection of the most common bacterial, fungal, and invertebrate pests and pathogens of M. rotundata larvae. Known pests of M. rotundata were detected, including members of the fungal genus Ascosphaera, the causative agent of chalkbrood. Co-infection of single brood cells by multiple Ascosphaera species was confirmed, with potential implications for chalkbrood disease management. The multiplex assay also identified DNA from more than 2,400 total species including multiple new predators and pathogenetic species not previously documented in associated with M. rotundata brood cells.

Macrozoobentos on the shelf of the Kronotsky Gulf

Data about the taxonomic composition and spatial distribution of bottom invertebrates of Kronotsky Gulf were obtained on results of bottom grab survey carried in September 2002. Analysis of the samples revealed 72 species of Polychaeta, 21 species of molluscs (Bivalvia), 17 species of crustaceans (mostly Amphipoda), 2 species of echinodermata (Echinoidea and Ophiuroidea). The average biomass in the depth range 25–200 m was 242±116 g/m2 where average density was 306±51 organisms/m2. The most high values of biomass were observed in the outlet parts of the rivers Zhupanova, Semyachik, Kronotskaya, where contribution of sea dollar Echinarachnius parma communities was principal. Despite fluctuations of the biomass of particular taxons during 50 years, the total biomass keeps stable (206–242 g/m2). Like in 1949 E. parma plays the main role in most bottom communities.

The chronic wound virome: phage diversity and associations with wounds and healing outcomes

Two leading impediments to chronic wound healing are polymicrobial infection and biofilm formation. Recent studies have characterized the bacterial fraction of these microbiomes and have begun to elucidate compositional correlations to healing outcomes. However, the factors that drive compositional shifts are still being uncovered. The virome may play an important role in shaping bacterial community structure and function. Previous work on the skin virome determined that it was dominated by bacteriophages, viruses that infect bacteria. To characterize the virome, we enrolled 20 chronic wound patients presenting at an outpatient wound care clinic in a microbiome survey, collecting swab samples from healthy skin and chronic wounds before and after a single, sharp debridement procedure. We investigated the virome using a virus-like particle enrichment procedure, shotgun metagenomic sequencing, and a k-mer-based, reference-dependent taxonomic classification method. Taxonomic composition, diversity, and associations to covariates are presented. We find that the wound virome is highly diverse, with many phages targeting known pathogens, and may influence bacterial community composition and functionality in ways that impact healing outcomes.

MinION™ Nanopore Sequencing of Skin Microbiome 16S and 16S-23S rRNA Gene Amplicons

Human skin microbiome dysbiosis can have clinical consequences. Characterizing taxonomic composition of bacterial communities associated with skin disorders is important for dermatological advancement in both diagnosis and novel treatments. This study aims to analyze and improve the accuracy of taxonomic classification of skin bacteria with MinION™ nanopore sequencing using a defined skin mock community and a skin microbiome sample. We compared the Oxford Nanopore Technologies recommended procedures and concluded that their protocols highly bias the relative abundance of certain skin microbiome genera, most notably a large overrepresentation of Staphylococcus and underrepresentation of Cutibacterium and Corynebacterium. We demonstrated that changes in the amplification protocols improved the accuracy of the taxonomic classification for these three main skin bacterial genera. This study shows that MinION™ nanopore could be an efficient technology for full-length 16S rRNA sequencing; however, the analytical advantage is strongly influenced by the methodologies. The suggested alternatives in the sample processing improved characterization of a complex skin microbiome community using MinION™ nanopore sequencing.

Alien flora of Oman: invasion status, taxonomic composition, habitats, origin, and pathways of introduction

We present the first inventory and status assessment of the alien flora of Oman, mainly based on field data collected from 1998 to 2021. The study provides (i) a comprehensive account of alien vascular plant species occurring in the wild in Oman, with information on their taxonomic composition. For each species information is given on (ii) invasion status (casual, naturalized or invasive), biogeography, habitat and life-form characteristics, and pathways of introduction. Further, we (iii) explain the differences in the alien species composition in different parts of the country, and (iv) analyse the drivers of plant invasions in Oman. Out of the 111 alien species reported (7.7% of the total Oman vascular flora), 34 species are casuals and 77 naturalized; of the latter seven are considered invasive. The moderate number of alien plant species is likely a result of the country’s arid climate, with extremely high summer temperatures and low annual precipitation in most of its area, and the relatively long isolation of the country. The families richest in alien plant species are Fabaceae (17 species), Asteraceae (14 species) and Poaceae (12 species). More alien plants were found in northern Oman (82 species) than in southern Oman (60 species), and very few species are recorded from the central desert (7 species). The main habitats colonized were man-made habitats, either ruderal or agricultural. Most species alien to Oman are native to South America (49 species) or North America (43 species). This inventory provides a knowledge base for developing a national management strategy for alien vascular plants in Oman.

Taxonomic composition and biodiversity of the gut microbiome from patients with irritable bowel syndrome, ulcerative colitis, and asthma

To date, the association of an imbalance of the intestinal microbiota with various human diseases, including both diseases of the gastrointestinal tract and disorders of the immune system, has been shown. However, despite the huge amount of accumulated data, many key questions still remain unanswered. Given limited data on the composition of the gut microbiota in patients with ulcerative colitis (UC) and irritable bowel syndrome (IBS) from different parts of Siberia, as well as the lack of data on the gut microbiota of patients with bronchial asthma (BA), the aim of the study was to assess the biodiversity of the gut microbiota of patients with IBS, UC and BA in comparison with those of healthy volunteers (HV). In this study, a comparative assessment of the biodiversity and taxonomic structure of gut microbiome was conducted based on the sequencing of 16S rRNA genes obtained from fecal samples of patients with IBS, UC, BA and volunteers. Sequences of the Firmicutes and Bacteroidetes types dominated in all samples studied. The third most common in all samples were sequences of the Proteobacteria type, which contains pathogenic and opportunistic bacteria. Sequences of the Actinobacteria type were, on average, the fourth most common. The results showed the presence of dysbiosis in the samples from patients compared to the sample from HVs. The ratio of Firmicutes/Bacteroidetes was lower in the IBS and UC samples than in HV and higher the BA samples. In the samples from patients with intestinal diseases (IBS and UC), an increase in the proportion of sequences of the Bacteroidetes type and a decrease in the proportion of sequences of the Clostridia class, as well as the Ruminococcaceae, but not Erysipelotrichaceae family, were found. The IBS, UC, and BA samples had signif icantly more Proteobacteria sequences, including Methylobacterium, Sphingomonas, Parasutterella, Halomonas, Vibrio, as well as Escherichia spp. and Shigella spp. In the gut microbiota of adults with BA, a decrease in the proportion of Roseburia, Lachnospira, Veillonella sequences was detected, but the share of Faecalibacterium and Lactobacillus sequences was the same as in healthy individuals. A signif icant increase in the proportion of Halomonas and Vibrio sequences in the gut microbiota in patients with BA has been described for the f irst time.

Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma

BackgroundThe significance of the relationship between the microbiota and diseases is increasingly being recognized. However, the characterization of tumor microbiome and their precise molecular mechanisms through which microbiota promotes hepatocellular carcinoma (HCC) development are still unclear.MethodsThe intrahepatic microbiota was investigated from tumor, normal adjacent tissues in 46 patients with HCC and normal hepatic tissues in 33 patients with hemangioma by 16S rRNA gene sequencing. Taxonomic composition differences in patients were evaluated using Linear discriminant analysis Effect Size (LefSe) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to predict microbial functional pathways. Associations between the most relevant taxa and clinical characteristics of HCC patients were analyzed by Spearman rank correlations. The effects of microbe on hepatic stellate cells (HSCs) activation and HCC progression were examined.ResultsWe observed intrahepatic microbiota disturbances by reduced microbial diversity in HCC. The tumor microbiota of the HCC patients with cirrhosis showed higher abundance of Stenotrophomonas maltophilia (S. maltophilia). S. maltophilia provoked senescence-associated secretory phenotype (SASP) in HSCs by activating TLR-4-mediated NF-κB signaling pathway, which in turn induced NLRP3 inflammasome complex formation and secreted various inflammatory factors in the liver, thus facilitating HCC progression in mice. Moreover, signs of SASP were also observed in the HSCs in the area of HCC with higher S. maltophilia enrichment arising in patients with cirrhosis.ConclusionsOur analysis of the hepatic microbiota revealed for the first time that patients with HCC exhibited a dysbiotic microbial community with higher S. maltophilia abundance, which induced the expression SASP factors of HSCs and cirrhosis in the liver, concurring in the process of hepatocarcinogenesis.

Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments

Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.

Ethno-botanical uses and taxonomic composition of some Aju Mbaise (Mbaise wraps)

This document focuses on the ethnobotanical uses and taxonomic composition of some Aju Mbaise (Mbaise wraps). A total of 31 plant species belonging to 24 families were identified in the wraps collected from the study area. These plants are used in the treatment of ailments such as hypertension, typhoid, malaria, boost fertility in females, post-partum (immediately after birth), treatment of diabetes, treatment of arthritis, and induce weight loss. Annonaceae family constituted 9.68% of the total plant family, followed by Acanthaceae, Combretaceae, Fabaceae, Malvaceae, and Rubiaceae with 6.45% each. Among the plant species, Cnestis ferruginea (Connaraceae) occurred in five wraps. This is followed by Alternanthera bettzickiana (Amaranthaceae), Craterispermum cerinanthum (Rubiaceae), and Napoleona imparalis (Lecythidaceae) found in four wraps while Acanthus montanus (Acanthaceae), Barteria nigritana (Passifloraceae), Nephrolepis exaltata (Nephrolepidaceae), Oxytenanthera abyssinica (Poaceae), Palisota hirsuta (Commelinaceae), Scleria naumanniana (Cyperaceae), and Sida rhomboidea (Malvaceae) are in three ailments each. These plant species and families with high occurrence are the most effectively used plant groups in the study for the treatment of these diseases.

Dynamics of changes in the dendrocenosis of quarter 26 «Champs Elysees» of the National Dendrological Park «Sofiyivka» of the NAS of Ukraine

Since the founding of the «Sofiyivka» Dendrological Park, over more than two centuries, the structure of the dendrocenosis and park compositions including the «Champs Elysees» (Quarter 26), located in the center of the park' s historic core changed. The changes were caused by a complex of biotic and abiotic factors that influenced the taxonomic composition of plants. The paper presents the results of a study of the dynamics of changes in the dendrocenosis of the quarter 26 «Champs Elysees», which will contribute to the preservation and restoration of the historic site of the ancient park, in particular its taxonomic composition.