Shannon Diversity Index Research Articles

Development of SSR markers for genetic diversity analysis and species identification in Polygonatum odoratum (Mill.) Druce based on transcriptome sequences.

Polygonatum odoratum (Mill.) Druce is a well-known traditional Chinese herb belonging to the Polygonatum. However, the understanding of the genetic diversity of this species at the molecular level is limited due to the lack of transcriptomic and genomic information. In this study, 37,387 unigenes were assembled based on the transcriptome sequencing of the rhizome of Polygonatum odoratum (Mill.) Druce., and 11,021 single- sequence repeats (SSR) motifs, mainly consisting of single-nucleotide repeats (44.44%), dinucleotides (31.06%), and trinucleotides (22.59%), were identified. Based on these SSR motifs, 9,987 primer pairs of SSR markers were designed and 68 SSR markers were randomly selected for verification, of which 21 SSR markers showed polymorphisms among the 24 Polygonatum odoratum germplasms. Ninety-four alleles were detected: the observed alleles ranged from 2 to 11, the effective alleles varied from 1.086 8 to 4.916 8, the Shannon diversity index was 0.173 2~1.749 7, and the polymorphism information content PIC ranged from 0.076 7 to 0.803 9. Based on our analysis of genetic diversity (SSR genotypes) and population structure, we divided the 24 germplasm resources into two groups, indicating that the germplasm with similar geographical origins can be grouped together. In addition, the primers 'YZ14' and 'YZ47' could effectively distinguished the related species: Polygonatum kingianum Coll.et Hemsl., Polygonatum sibiricum Red., Polygonatum cyrtonema Hua, Polygonatum zanlanscianense Pamp. and Polygonatum odoratum (Mill.) Druce. This is the first study in which a dataset of expressed sequence tag (EST)-SSR markers is constructed for the Polygonatum odoratum (Mill.) Druce, and these newly developed EST-SSR markers provided a very efficient tool for genetic relationship analysis, species identification and marker-assisted selection breeding of Polygonatum odoratum (Mill.) Druce.

Regenerative soil management practices no‐till and sheep grazing induce significant but contrasting short‐term changes in the vineyard soil microbiome

Societal Impact StatementWinegrape production is an essential cultural heritage and economic engine of many regions of the world. Regenerative management, which is gaining traction with industry and consumers alike, relies on soil biodiversity for agroecosystem function, reducing external inputs and increasing ecosystem resilience to climate change. We evaluated the effects of no‐till and sheep integration on vineyard soil biodiversity and soil ecosystem function. No‐till had stronger effects on microbial diversity, while sheep grazing stimulated microbial functioning. By providing a better understanding of the practices, we provide fundamental information for growers that want to embrace regenerative principles, ultimately contributing to the sustainability and resilience of the winegrape industry.Summary Regenerative management aims to optimize soil microbial function and diversity for enhanced agroecosystem functionality. Understanding the effects of management practices on soil microorganisms is crucial in the context of growing societal interest in this type of management. This study evaluated the short‐term effects of two soil conservation practices: sheep grazing and no‐till, on abundance, diversity, activity, and network complexity of prokaryotes and fungi in a vineyard soil. Four treatments were applied for 3 years: (1) grazed and tilled, (2) grazed and non‐tilled, (3) non‐grazed and tilled, and (4) non‐grazed and non‐tilled. We hypothesized that stacking of conservation practices (grazing and no‐till) would increase microbial diversity, function, and network complexity. Grazing had strong effects on microbial function, increasing the α‐glucosidase, β‐glucosidase, cellulase, phosphatase, and β‐xylosidase enzymatic activity by 82%, 48%, 61%, 39%, and 55%, respectively, compared to non‐grazed soils, while not causing significant changes in soil microbial diversity. Tillage had strong effects on soil prokaryotic and fungal diversity. For prokaryotes, significant interactions in alpha diversity were found between tillage and grazing, and between tillage and sampling location (tractor row and under vine). Fungal Shannon diversity index was higher in the subsoil (15–30 cm) while a significant interaction between depth, location, tillage, and grazing was found for the Chao‐1 index. Microbial network properties were only significantly affected by sampling depth. This study shows that the lack of disturbance in non‐tilled and non‐grazed soils resulted in a more diverse soil community, while grazing stimulated microbial function, thus showing a decoupling between diversity and function in vineyard soil ecosystems.

Abstract C082: Descriptive study of the vaginal microbiome in Hispanic populations in Houston and Puerto Rico with high-risk normal and cervical dysplasia

Abstract Objective Cervical cancer is a leading cause of cancer-related deaths in women worldwide, leading to over 340,000 deaths in 2022. The majority of cervical cancers are caused by the persistent infection of high-risk human papillomavirus (HPV). In the United States, Hispanic women are at increased risk of cervical cancer development and are more likely to die of the disease in certain geographical locations. Furthermore, prior research implicated an association between the vaginal microbiota and the risk of HPV infection and cervical dysplasia. This descriptive study aims to explore the vaginal microbiome profiles of Hispanic or Latino women at risk for HPV-induced cervical dysplasia or with cervical dysplasia residing in Houston and in Puerto Rico. MethodsCervical swab samples were collected from Hispanic patients in Houston IRB 2019-1059 (N = 93) and Puerto Rico IRB 1050411 (N = 118) during routine clinical visits on a prospective collection protocol. Swabs were acquired at the patient’s initial visit and subjected to 16S V4 rRNA gene sequencing for microbiome profiling. Through HPV genotyping via PCR, patients were categorized into three groups: having HPV 16, other high-risk HPV types (18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68), and “other”, comprised of low-risk HPV types, HPV negative, or unknown HPV status. Alpha and beta diversity were assessed using QIIME2. Microbiome composition was evaluated across different locations, HPV status, and disease status, followed by exploring alpha diversity between locations and disease status. The taxa species classification was performed using a custom classifier trained via a cervicovaginal-specific database. Samples were assigned to vaginal community state types (CSTs) using VALENCIA. Results Within the study cohort, 72% (N = 152) were classified as high-risk normal, and 28% (N = 59) had cervical dysplasia. HPV 16 was detected in 12% (N = 26), other high-risk HPV types in 33% (N = 70), while 55% (N = 115) of patients were classified as “other”. At the species level, the vaginal microbiota is dominated by Lactobacillus crispatus, Lactobacillus iners, and Trichomonas vaginalis as the top three abundant, regardless of the patient’s location, HPV status, and disease status. Alpha diversity between locations was 2.2 (1.4) for Houston and 1.6 (1.3) for Puerto Rico, as demonstrated by the Shannon Diversity Index. Alpha diversity was also observed between disease status, with a mean Shannon Diversity Index of 1.9 (1.4) for high-risk normal and 1.9 (1.1) for cervical dysplasia. The top three vaginal community state types were IV-B (32%), I (27%), and III (23%) for Houston, while the top three for Puerto Rico were III (34%), IV-B (31%), and I (21%). Conclusion The study examines the vaginal microbiome profiles of Hispanic women in Houston and Puerto Rico who are at risk for HPV-induced cervical dysplasia or already have cervical dysplasia. These findings provide insights into the vaginal microbiome composition, which plays a crucial role in cervical cancer development. Citation Format: D'Shaunique Walters, Molly El Alam, Timothy Harris, Tatiana Cisneros, Nadim Ajami, Jagannadha Sastry, Josefina Romaguera, Filipa Godoy-Vitorino, Stephanie Dorta-Estremera, Ann Klopp, Lauren Colbert. Descriptive study of the vaginal microbiome in Hispanic populations in Houston and Puerto Rico with high-risk normal and cervical dysplasia [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C082.

Establishment of methanogen bacterial interactions during the preweaning period of dairy cattle

Ruminant livestock are major contributors to anthropogenic methane emissions in the United States and worldwide. Enteric methane is generated by methanogenic archaea residing in ruminant digestive tracts. Information on when methanogens colonize the gut and when they begin to interact with bacteria during the early phases of the ruminant life cycle is less explored. The objectives of this study were (i) to investigate the composition of the methanogenic archaeal community at birth and through the weaning transition and (ii) to determine if and when the methanogenic archaea begin to interact with bacteria in the lower gut of neonatal dairy calves. Ten female Holstein calves (approximately 45kg birth weight) were enrolled in the study. Fecal samples were collected every two weeks (Wk 2, 4, 6, 8, 10, and 12) between birth and weaning and analyzed for methanogenic archaeal diversity via 16S rRNA amplicon sequencing and quantitative real-time PCR (RT-qPCR). Estimates of alpha diversity (Observed species, and Shannon diversity index) and beta diversity (weighted and unweighted UniFrac distances) showed significant differences (P < 0.05) between archaeal communities across timepoints. Both 16S rRNA amplicon sequencing and RT-qPCR analyses revealed Methanobrevibacter was the most prevalent genus at Wk2, Wk4, and Wk6, whereas Methanosphaera gradually increased with time and was most abundant at Wk10 and Wk12. Correlation analysis revealed that Methanobrevibacter and Methanosphaera were inversely correlated with each other and formed distinct cohorts with specific bacterial lineages similar to those reported in the mature rumen, thus revealing that these associations are established during the preweaning period. Therefore, the preweaning period presents a window of opportunity to interfere with early-life methanogenic colonization with the ultimate goal of reducing enteric methane emissions without perturbing ruminal function later in the life of dairy cattle.

Analysis of Mangrove Vegetation in Mesjid Raya Sub-District, Aceh Besar District

Mangrove ecosystems, characterized by their unique adaptation to intertidal zones along coastlines and river estuaries, play a crucial role in coastal ecology. This study investigated the composition and diversity of mangrove vegetation in Mesjid Raya District, Aceh Besar Regency. Employing a quantitative approach with purposive sampling, nine plots measuring 10x10 meters were established across three stations with varying physical environmental conditions, totaling 90 plots. Vegetation analysis revealed the presence of nine mangrove species belonging to five families. The Shannon diversity index (Ĥ) indicated a low level of species diversity within the studied mangrove communities.

PSLBII-7 Meta-analysis of the whole-body microbiota in cattle

Abstract Distinctive and self-sustainable microbial communities are present along the digestive, respiratory, and reproductive tracts, as well as in the mammary gland, and mucosal surfaces of the eye and hoof in cattle. Although the taxonomic and functional features of each of these communities have been relatively well characterized, this has been largely limited to the microbiome of an individual organ/site. However, recent developments suggest the presence of core taxa shared across the gut, respiratory, and reproductive microbiotas in cattle, and there is a need for a more holistic evaluation of microbial communities in and on cattle. Here, we performed a meta-analysis using all publicly available bovine 16S rRNA gene datasets deposited since 2019 to provide a holistic view of the whole-body microbiota. In total, we retrieved 16S rRNA gene sequences from 6,215 samples (53 studies originating from 29 different anatomical sites within beef and dairy cattle from Africa, Asia, Europe, South America, and North America. The 29 different anatomical sites including gut (ruminal fluid, ruminal tissues, feces, ileum, jejunum, cecum, colon and duodenum), respiratory (nasal cavity, deep nasopharynx, trachea and lung tissue), and reproductive tracts (female: vagina, endometrium and uterus; male: semen and prepuce), as well as the mammary gland (udder, teat apex, teat barrel, teat canal), eye (conjunctiva, ocular fluid and ocular surface swab), blood, hoof, joints and liver. Microbial community structure was distinct among different sample types (PERMANOVA, P < 0.05). Microbial richness differed by sample type (P < 0.0001) with mucosal surfaces (e.g. udder, eye and feet) having the greatest microbial richness followed by the gut. The lungs, liver, joints, semen and prepuce had the least microbial richness. Microbial diversity was greatest in the microbiota of the colon, cecum, teat apex, ruminal tissue and duodenum (Shannon diversity index > 5) while the liver (1.5), joint (2.3), and prepuce microbiota (2.7) were the least diverse. Bacillota had the highest relative abundance among phyla in the majority of microbial communities except for in the blood, prepuce, trachea and nasal cavity (dominated by Pseudomonadota), and liver (dominated by Fusobacteriota). The relatively most abundant genera across all samples were Mycoplasma (12.9%), Prevotella (3.9%), Bacteroides (2.4%), Escherichia (2.1%), Fusobacterium (2.0%), Ruminococcaceae UCG-005 (1.9%), Streptococcus (1.8%), Rikenellaceae RC9 (1.6%), and Corynebacterium (1.4%). However, their relative abundance varied greatly by body site, with the ocular and respiratory system samples dominated by Mycoplasma. Fusobacterium was relatively most abundant in the liver and semen, Corynebacterium in the mammary gland-associated samples, Bacteroides in the gut, and Streptococcus in the lower reproductive tract microbiota. Overall, our meta-analysis provides a comprehensive evaluation of the multiple bacterial communities in and on cattle, which will be useful for harnessing the whole-body microbiome to improve animal health and productivity.

Comparison of PSMA immunohistochemistry scoring systems to parametric [18F]PSMA-1007 PET/MRI in primary prostate cancer.

Quantification of PSMA expression via PSMA PET is well-established, however quantification of PSMA via immunohistochemistry (IHC) is not standardized. Our aim was to determine the most optimal PSMA IHC scoring system to quantify PSMA expression with PSMA PET as reference standard. Primary intermediate- and high-risk prostate cancer patients received an [18F]PSMA-1007 PET/MRI followed by radical prostatectomy. SUVmax, SUVmean and Ki of the prostate tumor was determined. Prostate tumors were stained with anti-PSMA antibodies and scored by 2 readers via 10 IHC scoring systems: histochemical score (H-score), immunoreactivity scorepredominant intensity (IRSpredominant intensity), IRS classificationpredominant intensity, IRSmean intensity, IRS classificationmean intensity, Allred score, predominant expression pattern, Shannon diversity index (SDI), percentage negatively stained cells and total percentage positively stained cells. Spearman's rank correlation coefficients (ρ) were calculated between PET parameters and IHC scoring systems. Interreader agreement for the IHC scoring systems was measured by the intraclass correlation coefficient (ICC). Fifty tumors in 46 patients were analysed. H-score had the best correlation with SUVmax (ρ 0.615 p < 0.0001) and SUVmean (ρ 0.570, p < 0.0001) and the second best correlation with Ki (ρ 0.411, p = 0.0030). SDI had the best correlation with Ki (ρ -0.440, p = 0.0014) and the second best correlation with SUVmax (ρ -0.516, p = 0.0001) and SUVmean (ρ -0.490, p = 0.0003). A moderate interreader agreement was observed for H-score (ICC 0.663, 95% CI 0.495-0.797) and SDI (ICC 0.546, 95% CI 0.354-0.725). H-score had the best correlation with PSMA PET quantification and an acceptable interreader agreement. Therefore, we deem H-score the most optimal PSMA IHC scoring system.

Seasonal variations in the structure of avian community in Zambezi riparian forest

Among the different biomes in southern Africa, tropical riparian forests appear to be especially rich in terms of biodiversity, but little is known about avian communities occupying these forests. In this paper, bird counts were conducted in May, July–August, and October–November in 2013 and 2014. The line transect method was used. A transect 16.6 km long was designed along the Zambezi River between S 17.4975 E 24.3478 and S 17.4874 E 24.447. In total, 146 bird species were recorded. The number of species detected each season varied from 95 to 100. The number of dominant species was consistently low, varying between 2 and 3 depending on the month. However, the cumulative dominance and the dominance index were much higher in the dry season (May–August) than in the wet season (October–November). Two species were dominant each month: Euplectes axillaris and Pycnonotus tricolor. Vidua macroura and Estrilda astrild were dominant only in October, while Streptopelia capicola was dominant only in May. The group of subdominants was much more diverse than dominants and included 13 species. The Shannon diversity index increased between July and November from 3.45 to 4.05 but Simpson's diversity index did not show any seasonal trend. Pielou's evenness index was higher in the wet season (0.82–0.88) than in the dry season (0.76–0.79). The proportions of the main feeding guilds were much the same throughout the year, except for November, when the proportion of insectivores markedly increased, while that of granivores decreased. Riparian forest corridors in urbanized environments may be viewed as main instruments for offsetting the negative effects of habitat loss and fragmentation. Dataset published through GBIF (DOI: 10.15470/0ssr1v)

SPATIAL DISTRIBUTION AND ASSESSMENT OF PUBLIC GREEN SPACES IN AN URBAN SETTLEMENT

The article examines the current land use of green spaces as an integral part of the urban economy through the example of a city in central Ukraine, Kropyvnytskyi. It analyses the regulatory framework for the functioning of green spaces. The study also includes an analysis of the geospatial distribution of public green spaces and their structure by number and area in the regional centre. The authors estimate the green areas covered with tree plantations based on vegetative indicators using remote sensing data. The Normalised Difference Vegetation Index (NDVI) allowed for clarifying the boundaries of green areas, their area, and the density of green mass of vegetation. This index helps to identify the spatial-temporal trends of vegetation, which are necessary to support scientific-grounded management decisions for city governance. The results of determining the NDVI are presented in the example of the park-monument of landscape art ‘Dendropark’. For vegetation in good condition, its value exceeds 0.7, corresponding to 58 % of the area. The Shannon Diversity Index has been used to assess the distribution of land use types in the green areas of general use. We identified six types of green area land use in Kropyvnytskyi city and performed the index calculations according to these types of land use. The calculation of the provision of public green spaces for city residents confirmed its low value compared to the standards. The research’s results determined that Kropyvnytskyi city needs to create new green zones, preserve existing ones, inventory, and develop a database of all green areas. Planting areas of new residential buildings and applying the experience of other countries to increase green areas due to alternative landscaping types (vertical landscaping, green roofs, and others) will allow for an expansion in the green areas of settlements, especially in large cities. The practical importance of the research results is their potential use for creating a strategy to develop and preserve green plantings in the city of Kropyvnytskyi for future years. Keywords: vegetation index, land use, diversity index, green areas, parks.

Phytoseiid Mites: Trees, Ecology and Conservation

The highly variable ’leafscapes’ of plants across the world represent billions of square metres of mite habitat. The phytoseiid mites (Acari: Phytoseiidae), an extremely species-rich group of mostly generalist predators, are providers of ecosystem services for humanity worth many hundreds of millions of dollars annually by helping suppress phytophagous mites and insects in forests, agro-ecosystems, shade-houses and home gardens. In this study, the phytoseiid mite assemblages on the leaves of four species of common tree species, namely oak (Quercus cerris var. cerris), poplar (Populus deltoides, P. nigra) and walnut (Juglans regia), were compared. The three data sets used were generated in three independent seasonal studies in Samsun Province, Türkiye, between 2018 and 2022. In total, mite species in 18 families, including 15 families on walnut, were recorded. Nineteen phytoseiid species in 13 genera, Amblydromalus, Amblyseius, Euseius, Kampimodromus, Neoseiulella, Neoseiulus, Paraseiulus, Phytoseius, Transeius, Typhlodromina, Typhlodromips, Typhlodromus and Typhloseiulus, were collected. Only Eusieus amissibilis was collected from all three tree genera, whereas 14 species were collected from only one tree genus. Shannon diversity and Jaccard similarity indexes were calculated for mite families and phytoseiid genera and species. Potential reasons for the observed differences in the phytoseiid assemblages on the different host trees are explored in depth. In the ‘big picture’, global biodiversity, likely including many undescribed phytoseiid species, is threatened by widespread habitat degradation and destruction, especially in the tropics, and accelerating climate change, and rapidly stopping them is imperative.

Influence of different stocking densities of pearlspot (Etroplus suratensis) on plankton diversity indices of biofilm-based rearing system

Aim: Biofilm-based aquaculture systems, proven cost-effective, reduce the need for expensive supplementary feed. The biofilm acts as a natural planktonic food source for reared organisms. Previous research highlighted the influence of fish stocking density and biomass on plankton diversity in different aquaculture settings, underscoring the significance of these factors in biofilm-based systems. Hence, the present study attempted to understand how varying stocking densities of pearlspot (Etroplus suratensis) influence plankton diversity indices in the biofilm-based aquaculture system. Methodology: The present experiment was designed in 5 Practical Salinity Unit (PSU) brackishwater with soil-bottomed FRP circular (500 L) tanks for 60 days. The sugarcane bagasse was used as a substrate forbiofilm production after fertilization with cow dung, urea, and lime. Fries of pearlspot (4.67 ± 0.04 mm 1.71 ± 0.03 g-1) were stocked at four different stocking densities in triplicates viz T1 (50 nos); T2 (100 nos), T3 (150 nos) and T4 (200 nos) fish fry m-3 in the biofilm-based rearing system. Plankton samples were collected from water and biofilm deposited on the substrate and analyzed for diversity indices. The Shannon Diversity Index, Simpson Diversity Index, Simpson Dominance Index, and Margalef Richness Index were used to compute the plankton diversity indices in different treatments using standard equations. Results: In the current investigation, lower stocking densities with lower fish biomass were associated with significantly higher (P≤0.05) Shannon Diversity Index, Simpson Diversity Index, and Margalef Richness Index in water. In contrast, the Simpson Dominance Index in water showed a significantly lower (P≤0.05) value for treatments with lower fish biomass than for treatments with higher biomass. Interpretation: The values obtained for various diversity indices indicated that a biofilm-rearing system with lower E. suratensis biomass produced more planktonic abundance, evenness, and species richness. Key words: Biofilm, Pearlspot, Plankton diversity, Stocking density

Community structure, species diversity and biomass of trees in Tranum Forest Reserve, Raub, Pahang

This study was conducted at the Tranum Forest Reserve, Raub, Pahang to determine the community structure, species diversity and biomass of trees in the area. Four study plots, each measuring 25 m × 20 m, were established at the study site, which covered a total area of 0.2 ha. All trees with diameter at breast height (DBH) of 5 cm and above were measured and recorded. A total of 175 trees was enumerated in the study plots, comprising 106 species and 79 genera from 40 families. The largest family was Lauraceae, represented by 11 species from six genera, followed by Myrtaceae with eight species from one genus. Tree species diversity of the study area was high, as reflected by a Shannon Diversity Index (H’) value of 4.49 (Hmax = 4.66). Margalef Richness Index (R’) and Shannon Evenness Index (E) showed values of 20.33 and 0.84, respectively. The most important family, based on the highest Family Important Value Index (FIVi), was Dipterocarpaceae, with a value 17.31%. Shorea platyclados was the most important species with Important Value Index (IVi) of 17.04%. The tree density of the study area was 875 indidivuals per hectare (ind/ha), with Lauraceae being the densest family at 85 ind/ha. Vitex gamosepala was the densest species at 40 ind/ha. The total basal area of trees was 66.23 m2/ha, with Dipterocarpaceae showed the highest basal area of 31.69 m2/ha and Shorea platyclados had the highest basal area of 31.69 m2/ha at species level. The total biomass of trees was estimated at 1,307.56 t/ha, of which the above ground biomass and the below ground biomass were 1,091.33 t/ha and 216.23 t/ha, respectively. Dipterocarpaceae contributed the highest biomass with an estimate of 743.83 t/ha and Shorea platyclados showed the highest biomass at species level with 743.83 t/ha.

Similar In Vitro Ileal Fermentation Outcomes Validate the Use of a Pig Ileal Inoculum in an In Vitro Fermentation Assay for the Adult Human

BackgroundAn in vivo/in vitro ileal fermentation assay using growing pigs has shown important fermentability and organic acid production. This assay could be used to study human foods but needs validation. ObjectivesA pig inoculum for studying human ileal fermentation was used to compare the in vitro fermentation of fiber substrates using ileal inocula prepared from growing pigs or human ileostomates. MethodsTen pigs (19 ± 4.5 kg bodyweight, mean ± standard deviation) received a diet containing human foods. After 2 wk, ileal digesta were collected 5 h postmeal. Five recruited human ileostomates incorporated the same human foods into their diet for a week before consuming 2 meals similar to the pigs’ diet. Ileal effluents were then collected from 2 to 6 h postmeal. The porcine ileal digesta and human ileal effluents were used for microbial analysis and in vitro fermentation of arabinogalactan, fructooligosaccharides, and pectin. ResultsThe in vitro organic matter fermentability of arabinogalactan, fructooligosaccharides, and pectin was similar (P > 0.05) between the pig and human ileal inocula (34 ± 2.13% on average). Regardless of substrates, the propionic and lactic acid production was similar between humans and pigs (P > 0.05). Ninety percent of the ileal bacterial genera were found in similar (P > 0.05) numbers in pigs and human ileostomates, which accords with the similar (P > 0.05) Shannon diversity index and predicted metabolic activity. However, some of the most abundant genera were different between species, such as Granulicatella which had 83-fold greater (P ≤ 0.05) numbers in human ileostomates, and Lactobacillus had 272-fold greater (P ≤ 0.05) numbers in pigs. ConclusionsThe in vitro ileal fermentation patterns were similar across species despite some ileal microbial compositional differences, suggesting that the growing pig could be used as a model to provide an ileal inoculum for studying ileal fermentation in adult humans.This trial was registered at the Australian New Zealand Clinical Trials registry as ACTRN12622000813785.

Snake diversity, occupancy, and detection on Thailand's largest university campus.

More than 240 species of snake have been described from Thailand, yet basic natural history and ecology for this group of animals remains scarce in human disturbed environments despite conservation and human medical significance of them in these habitats. We studied snake diversity at Walailak University from March to December 2023, the largest university campus in Thailand (1525 hectares) through standardized walking surveys, opportunistic notifications and observation, road surveys, and traps and evaluated diversity using the Shannon diversity index (H), Pielou's evenness of species (J), detection probabilities (p), and occupancy probabilities (ψ). We observed 195 snakes (21 species, 7 families) at Walailak University and overall snake diversity (H = 2.60) and evenness (J = 0.85) were quite high, although specific site diversity (range H = 0-1.94) and evenness (range J = 0.67-0.91) within the university were variable. The probability of detecting snakes (range p = .10-.40) increased with increasing humidity and decreased with increasing amount of rain, temperature, and wind; site occupancy probability decreased with increased canopy height and increased with increased distance to buildings, increased canopy height loss, increased distance to roads, and increased distance to water. Our findings of relatively high snake diversity, presence of snake species potentially dangerous to humans (six species), and protected snake species (Thailand WARPA and international CITES, five species) suggest significant potential for conservation and further research at Walailak University and other campuses in Thailand.

Maiden study on fish diversity of the Diring River in Baksa District, Assam, India

The Northeast India has several natural water resources that support a variety of aquatic fauna. However, many parts of the region have remained unexplored for ichthyofauna. Research on the diversity of fishes in large water bodies has received significant attention from many researchers in the region. In contrast, studies on small stream rivers are very scant. Therefore, the present study aims to record the diversity of fish fauna in the small stream Diring River of Baksa District, Assam. In this survey, 27 species of fishes were recorded from five study sites. The dominant family was Cyprinidae, comprising 48% of the total fish species. The conservation status of the majority of species was Least Concern (88.8%) followed by Near Threatened (3.7%) and Vulnerable (3.7%). However, conservation status of 3.7% of the fish species was not evaluated by IUCN. The Shannon diversity index ranged from 1.5 to 2.6, the evenness index from 0.84 to 0.98, and the richness index from 1.1 to 2.6, indicating a good status of ichthyofaunal resources in the study sites. Since there were no existing records on the fish diversity of the Diring River, this maiden study might serve as baseline information for further research.

Integrating ecosystem services supply-demand balance into landscape ecological risk and its driving forces assessment in Southwest China

The supply-demand balance of ecosystem services (ES) plays an important role in mitigating regional ecological risks and optimizing landscape patterns. However, traditional landscape ecological risk (LER) assessments consider the potential loss of ES supply while ignoring the supply–demand coupling relationship, and fails to reveal the actual situation of ecological risk. To fill this gap, taking the Southwest China (SWC) as an example, this study proposed an improved LER assessment method that focuses on ES supply-demand balance, and analyzed the spatio-temporal characteristics of LER and its driving factors in the SWC from 2000 to 2020 by using hotspot analysis, geo-detectors and geographical temporally weighted regression models. The results show that (1) the comparison results with the traditional LER evaluation method demonstrated the improved method's superior rationality and reliability. The overall LER of the SWC over the past 20 years displayed a fluctuating trend, with a spatial clustering pattern of high in the northeast and low in the southwest. (2) Human activities explained the relatively high spatial heterogeneity in high-risk areas, while in low-risk areas it was mainly the interaction of natural factors and landscape structural. Meanwhile, obvious temporal non-stationary was identified in the evolution of the key factors. The positive effects of land use intensity and landscape fragmentation gradually weakened, while the negative effects of Shannon diversity index gradually increased. The results can provide theoretical support and policy recommendations for ecosystem conservation and high-quality urban development in the SWC.

Impact of species selection on plant community, sod tensile strength, and translocation rooting of a pollinator‐garden sod

AbstractInterest in pollinator gardens is increasing to address pollinator decline. The establishment of perennial native plants often takes a few years and establishment projects are often lost to competition from unwanted weedy vegetation. Mature sod of pollinator‐serving, native plants that is free of weeds would be highly desirable to conventional turfgrass sod consumers, thus offering a new revenue stream for traditional sod producers. The objective of this study is to evaluate the influence of four foundational species treatments on 3‐year floral biodiversity of pollinator‐serving plants, sod tensile strength, and transplant rooting strength. Results suggest that polycultures of pollinator‐serving forbs can produce a marketable sod with sufficient tensile strength for lifting and translocating and sufficient ability to establish once relocated. Sod tensile strength, however, is insufficient for lifting when the plant community is not grown over plastic or does not contain a high‐shoot density or rhizomatous foundation species such as hard fescue (Festuca longifolia Thuill.) or common yarrow (Achillea millefolium L.). Unfortunately, adding hard fescue or common yarrow markedly reduces the Shannon diversity index and species richness. The force needed to lift transplanted sod after 3 months was 5553 to 6969 N m−2 regardless of foundation species treatment and was numerically higher than the force reported by previous researchers to lift sod of various turfgrass species. Collectively, the data suggest that the best balance between preserving floral biodiversity and maximizing sod handling integrity would be approached by establishing pollinator‐serving forbs alone or with a blend of native grasses over plastic.

Nanopore R10.4 metagenomic detection of blaCTX-M/blaDHA antimicrobial resistance genes and their genetic environments in stool

The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun metagenomic sequencing (Nanopore-SMS) latest V14 chemistry to detect blaCTX-M and blaDHA genes from healthy stools. We test 25 paired samples characterized with culture-based methods (native and pre-enriched). Antimicrobial resistant genes (ARGs) are detected from reads and meta-assembled genomes (MAGs) to determine their associated genetic environments (AGEs). Sensitivity and specificity of native Nanopore-SMS are 61.1% and 100%, compared to 81.5% and 75% for pre-enriched Nanopore-SMS, respectively. Native Nanopore-SMS identifies only one sample with an AGE, whereas pre-enriched Nanopore-SMS recognizes 9/18 plasmids and 5/9 E. coli chromosomes. Pre-enriched Nanopore-SMS identifies more ARGs than native Nanopore-SMS (p < 0.001). Notably, blaCTX-Ms and blaDHAs AGEs (plasmid and chromosomes) are identified within 1 hour of sequencing. Furthermore, microbiota analyses show that pre-enriched Nanopore-SMS results in more E. coli classified reads (47% vs. 3.1%), higher differential abundance (5.69 log2 fold) and lower Shannon diversity index (p < 0.0001). Nanopore-SMS has the potential to be used for intestinal colonization screening. However, sample pre-enrichment is necessary to increase sensitivity. Further computational improvements are needed to reduce the turnaround time for clinical applications.

Response of Surface Runoff Evolution to Landscape Patterns in Karst Areas: A Case Study of Yun–Gui Plateau

To control and improve the phenomena of rocky desertification and soil erosion in karst landform areas, which are caused by a series of human factors that include social and economic development and human activities, China has successively introduced many policies, resulting in spatial and temporal changes in the landscape pattern of the southern karst area. In this study, land use transfer intensity maps, the grid method, the sample line method, the semivariogram method, and the Spearman analysis method are used to explore the spatial and temporal evolutions in surface runoff as responses to landscape pattern and policy factors in karst landform area. Therefore, this study provides theoretical and policy support for improving the regional landscape structure, optimizing the landscape layout, introducing regional policies, reducing surface runoff, and alleviating soil erosion. The results show that the best scale for the study of landscape patterns in the southern karst area is 3000 m. Forests are the land type that make up the highest proportion in the southern karst area, and they have the strongest interception capacity for surface runoff. The spatial and temporal distributions of the surface runoff are significantly different, and urban expansion has led to an increase in impervious runoff year over year. Runoff is positively correlated with the Shannon diversity index (SHDI), patch density (PD), and landscape shape index (LSI). The stronger the landscape heterogeneity, the more runoff. DIVISION is positively correlated with forest runoff and negatively correlated with other land types. The higher is the degree of aggregation of impervious patches, the higher the regional runoff rate. The more dispersed the forest patches are, the smaller the area proportion, and the greater the runoff. In addition, policy factors have a significant impact on surface runoff.

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994-2018) and four hyperendemic Lake Victoria fishing communities (2011-2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.