Shannon Diversity Index Research Articles

Gut microbiota in preterm infants receiving breast milk or mixed feeding.

Preterm birth is the leading cause of mortality in newborns, with very-low-birth-weight infants usually experiencing several complications. Breast milk is considered the gold standard of nutrition, especially for preterm infants with delayed gut colonization, because it contains beneficial microorganisms, such as Lactobacilli and Bifidobacteria. To analyze the gut microbiota of breastfed preterm infants with a birth weight of 1500 g or less. An observational study was performed on preterm infants with up to 36.6 wk of gestation and a birth weight of 1500 g or less, born at the University Hospital Dr. José Eleuterio González at Monterrey, Mexico. A total of 40 preterm neonates were classified into breast milk feeding (BM) and mixed feeding (MF) groups (21 in the BM group and 19 in the MF group), from October 2017 to June 2019. Fecal samples were collected before they were introduced to any feeding type. After full enteral feeding was achieved, the composition of the gut microbiota was analyzed using 16S rRNA gene sequencing. Numerical variables were compared using Student's t-test or using the Mann-Whitney U test for nonparametric variables. Dominance, evenness, equitability, Margalef's index, Fisher's alpha, Chao-1 index, and Shannon's diversity index were also calculated. No significant differences were observed at the genus level between the groups. Class comparison indicated higher counts of Alphaproteobacteria and Betaproteobacteria in the initial compared to the final sample of the BM group (P < 0.011). In addition, higher counts of Gammaproteobacteria were detected in the final than in the initial sample (P = 0.040). According to the Margalef index, Fisher's alpha, and Chao-1 index, a decrease in species richness from the initial to the final sample, regardless of the feeding type, was observed (P < 0.050). The four predominant phyla were Bacteroidetes, Actinobacteria, Firmicutes, and Proteobacteria, with Proteobacteria being the most abundant. However, no significant differences were observed between the initial and final samples at the phylum level. Breastfeeding is associated with a decrease in Alphaproteobacteria and Betaproteobacteria and an increase of Gammaproteobacteria, contributing to the literature of the gut microbiota structure of very low-birth-weight, preterm.

Effect of Integrated Landscape Characteristics Around Chaohu Lake on River Water Quality Based on Watershed Units

Considering the impact of differences in watershed characteristics on river water quality, with the Chaohu Lake Basin as the research object, based on the data of water quality, meteorology, topography, soil, and remote sensing images of the river monitoring points from October 2019 to September 2020, the watershed unit at each monitoring point was divided through digital terrain analysis, and the comprehensive landscape characteristics based on the watershed unit were explored through the comprehensive use of correlation analysis, redundancy analysis, and multiple regression analysis to investigate the influence of comprehensive landscape characteristics based on watershed units (including land use, climate, topography, soil, etc.) on the water quality of rivers around Chaohu Lake. The results showed that:① the water quality of rivers around Chaohu Lake had large spatial differences, with the main pollutants being total nitrogen and ammonia nitrogen. Most of the rivers had total nitrogen concentrations exceeding the Class V water quality standards, and the areas with serious nitrogen and phosphorus pollution were concentrated in the urban area of Hefei and the surrounding rivers, as well as in the middle and lower reaches of the Fengle and Hangbu Rivers. ② The comprehensive landscape characteristics of the watershed unit had a significant impact on the river water quality. Among them, the proportion of built-up land, the density of patches, the dispersion and juxtaposition index, and the Shannon diversity index were positively correlated with the water quality indicators, whereas the proportion of forest and grassland and the spreading index were negatively correlated with the water quality indicators. ③ In different seasons, the effect of the integrated landscape characteristics of the watershed unit on river water quality was stronger in the wet season than in the dry season, which was mainly caused by the difference in precipitation in the dry and wet seasons.

Disease Occurrence and Climatic Factors Jointly Structure Pomelo Leaf Fungal Succession in Disturbed Agricultural Ecosystem.

For perennial plants, newly emerged organs are fresh hot spots for environmental microbes to occupy and assemble to form mature microbial communities. In the microbial community, some commensal fungi can play important roles in microbial succession, thus significantly improving host plant growth and disease resistance. However, their participating patterns in microbial assembly and succession remain largely unknown. In this study, we profiled the fungal community and found a similar fungal succession pattern of spring-emerged leaves from March to October in two pomelo orchards. Specifically, the fungal species, tracked on the old leaves, dominated the spring leaves after emergence and then decreased in relative abundance. This reduction in priority effects on the spring leaves was then followed by an increase in the number of observed species, Shannon and phylogenetic diversity indices, and the pathogen-associated fungal groups. In addition, we found that the temporal fungal succession on the spring leaves highly correlated with the disease occurrence in the orchards and with the temperature and precipitation variation from spring to summer. Of the pathogen-associated fungal groups, an increase in the relative abundance of Mycosphaerellaceae, hosting the causal agent of citrus greasy spot, correlated with the occurrence of the disease, while the relative abundance of Diaporthaceae, hosting the causal agent of melanose, was extremely low during the fungal succession. These results confirm that the two kinds of pathogen-associated fungal groups share different lifestyles on citrus, and also suggest that the study of temporal fungal succession in microbial communities can add to our understanding of the epidemiology of potential plant pathogens.

Insights into Gut Microbiome Composition in Hidradenitis Suppurativa: A Comprehensive Examination of Dietary Habits and Environmental Influences.

This study explores the relationship between dietary habits, environmental influences, and gut microbiome composition in individuals with hidradenitis suppurativa (HS), a chronic inflammatory skin condition. A cohort of 80 participants, equally divided into HS patients and healthy controls, was assessed through comprehensive questionnaires capturing demographics, dietary habits, and other health-related information. Fecal samples were collected and analyzed using next-generation sequencing to examine microbiome composition. Despite previous studies suggesting gut dysbiosis in HS, this research found no significant differences in alpha-diversity and Shannon diversity index between the groups. However, significant disparities in dietary habits were observed, with HS patients showing higher sugar and milk consumption. The study also identified a significant correlation between coffee consumption and the presence of certain bacterial genera. While the study did not reveal major differences in microbiome diversity, the findings on dietary habits and specific microbiome components suggest potential targets for therapeutic intervention. These results underscore the importance of further research into the gut-skin axis and its role in HS, aiming to enhance management strategies through dietary modifications and lifestyle interventions.

Multilevel Change of Urban Green Space and Spatiotemporal Heterogeneity Analysis of Driving Factors

Analyzing the change trend of urban green space (UGS) and exploring related driving forces can provide scientific reference for sustainable development in rapidly urbanizing areas. However, the spatial and temporal driving mechanisms of the drivers on UGS patterns at different scales are still not deeply understood. Based on the GlobeLand30 land cover data, nighttime lighting data and spatial statistics from 2000 to 2020, this study analyzed the size, shape and diversity of UGS in Guangzhou at the urban level, gradient level and township level with multiple landscape indices. Diversity means the richness of UGS patch types. The selected indices include percent of landscape (PLAND), largest path index (LPI), landscape shape index (LSI), aggregation index (AI) and Shannon’s diversity index (SHDI). The spatiotemporal heterogeneity of the drivers was then explored using the spatiotemporal weighted regression (GTWR) method. Results showed the following: (1) During 2000−2020, the total amount of UGS in Guangzhou increased slightly and then decreased gradually. UGS was mainly transferred into artificial surfaces (lands modified by human activities). (2) The UGS landscape showed a non-linear trend along the urban–rural gradient and fluctuated more in the interval of 20–60% urbanization level. PLAND, LPI and AI decreased significantly in areas with higher levels of urbanization. LSI increased and SHDI decreased significantly in areas with lower levels of urbanization. At township level, the landscape indices showed significant spatial autocorrelation. They transformed from discrete changes at the edge and at the junction of the administrative district to large-scale aggregated change, especially in northern areas. (3) The size of UGSs was mainly influenced by natural factors and population density, but their shape and diversity were mainly influenced by socio-economic factors. More regular shapes of green patches were expected in higher urbanization areas. Population agglomeration positively influenced green space patterns in the northeastern and southern regions (Zengcheng, Conghua and Nansha). Meanwhile the negative influence of urban expansion on the green space pattern in the central and southern regions decreased over time. This study contributes to an in-depth understanding of how the key factors affect the different changes of UGS with time and space and provides methodological support for the long-term zoning planning and management of UGS.

Prospective evaluation of the breast microbiome and tumor microenvironment-related biomarkers of response to neoadjuvant systemic therapy in triple negative breast cancer.

TPS615 Background: Predictive biomarkers of response to combination chemotherapy and immune-checkpoint inhibitors are urgently needed to tailor treatment recommendations for patients with early-stage triple negative breast cancer (eTNBC). Our group has demonstrated that tumour-associated microbiota in primary breast tumours represent promising and novel candidate biomarkers for patients with breast cancer. We aim to prospectively interrogate the breast cancer microbiome and tumour microenvironment (TME) of eTNBC treated with neoadjuvant chemo-immunotherapy, and correlate with clinical outcome. Methods: Trial design: This prospective translational biomarker study is enrolling patients with eTNBC suitable for standard neoadjuvant systemic therapy followed by definitive surgery. The primary objective is to evaluate the change in breast cancer microbiome composition pre- and post-therapy. Secondary objectives include correlation of the breast microbiome with pathologic complete response (pCR) and survival outcomes, tumor infiltrating lymphocytes (TILs), PDL-1 and immune subset analysis, extracellular vesicles analysis and analysis of gut microbiome. Tumor tissue samples will be collected at baseline (mandatory research biopsy) and at the time of surgery. Microbiome evaluation will be conducted using metagenomic sequencing to assess changes in the relative abundance of microbial taxa. Blood and stool samples will be collected and analysed at baseline, on-treatment, at the time of surgery and post-operatively for secondary endpoints. Statistical analysis: Hierarchical clustering of samples based on relative abundance of the operational taxonomic units (OTUs) with sample composition at family and genus level will be performed. Alpha Diversity (Shannon Diversity Index) and Beta Diversity (Jaccard Similarity Index) will be analysed. Principal component analysis (PCA) and Random Forest analysis will be performed for classification and clustering analysis. Comparison of taxa or functions between clinical cohorts will be performed (two tailed Z test) and corrected using the false discovery rate to determine Q-values. Thirty patients will be recruited over 18-24 months. Current status: This University College Cork sponsored trial received ethics approval from the CREC in January 2024 and recruitment is ongoing. Those interested can contact uccctg@ucc.ie. This trial will provide a deeper insight into the potential role of the local breast microbiome as a predictive biomarker for response to neoadjuvant therapy in patients with eTNBC. The results will guide further studies exploring optimal immunomodulatory combinations for the treatment of TNBC and may provide evidence regarding future therapeutic targeting of the breast cancer microbiome.

A pan-tumor prospective translational, Irish study, investigating the association of gut microbiome (GM) diversity with pathological complete response (pCR) after neoadjuvant treatment in early stage breast, rectal, and esophageal cancers.

TPS3188 Background: The gut microbiome (GM) is thought to influence host immunity by modulating multiple immunologic pathways. Studies have suggested that dysbiosis of the GM confers a predisposition to certain malignancies and influences response to immune checkpoint inhibitors. However, little is known about how the GM diversity influences complete pathological response to neo-adjuvant therapy in gastrointestinal (GI) and breast tumors. We hypothesize that a more diverse GM constitution at baseline will lead to improved pathological response at the time of definitive surgery. Methods: This is a cross institutional multi-centre Irish translational study investigating the impact of the GM diversity on the efficacy of neo-adjuvant therapy in GI and breast cancers by assessing its association with pathological response. The study population includes pts with early-stage breast, rectal or esophageal cancers commencing neo-adjuvant therapy (including chemotherapy, immunotherapy and chemo-radiation) and planned for definitive surgery. Exclusion criteria include prior allogenic tissue/solid organ transplantation and prior receipt of anti-cancer therapy. The study assessments will include fecal sampling of the GM prior to neo-adjuvant therapy, upon completion and again six months post completion of therapy. Fecal samples will be analysed by 16S RNA sequencing. Pathological response will be examined at time of surgery and patients will be classified as responders (complete pathological response) or non-responders. The primary endpoint of the study is to examine the association between the GM diversity and pathological response. Exploratory analysis will include the assessment of the association between cf-DNA and the GM diversity as well as an assessment of the association between cf-DNA at baseline and pCR. 120 patients will be recruited over 18 months. Species richness (Alpha Diversity) will be analysed using the Shannon diversity index and Jaccard similarity index will be used to calculate beta diversity. Following planned study recruitment, classification and clustering analysis will be performed with Principal Component Analysis (PCA) and Random Forest analysis. To assess the primary endpoint the association between GM and complete pathological response will be examined using logistic regression analysis adjusting for potential confounding factors in the final statistical analysis. Adjusted odds ratios (OR) and 95% confidence intervals will be presented. This is expected to read out in early 2025. Recruitment is ongoing, with 14 pts recruited to date. We demonstrate that it is feasible to accrue to translational studies in Ireland and we have streamlined screening and recruitment pathways to improve our methodology and recruitment numbers.

Psychoneurological symptoms, inflammatory biomarkers and gut microbiome richness and diversity in individuals receiving hematopoietic cell transplantation (HCT).

e24053 Background: Hematopoietic Stem Cell Transplantation (HCT) is a potentially curative treatment for certain hematologic cancers. Although survival rates are markedly higher than in the past, there are a growing number of long-term HCT survivors who are at risk for short and long-term sequela, which can negatively affect quality of life. Psychoneurological (PN) symptoms are common occurrences associated with heightened inflammation in other cancers and chronic conditions. Emerging research links the gut microbiota to inflammatory biomarkers and suggests that gut-microbiota-brain crosstalk impacts the severity of psychoneurological symptoms among HCT recipients. Methods: This longitudinal descriptive study investigated the relationship among a cluster of PN symptoms (pain, fatigue, and depression), inflammatory biomarkers (IL-6, IL-10, C-reactive protein (CRP), and microbiota diversity measures (Shannon and Chao Beta diversity indexes) in 55 individuals receiving HCT for a hematologic malignancy. The time periods examined covered pre-transplant, 30-days, and 100-days following transplant. The PN symptoms were collected through self-reported questionnaires via computer with assistance from study staff, along with blood samples and stool specimens obtained at each study visit. Inflammatory marker values were log-transformed when used as dependent variables. Gut microbiota samples were analyzed using 16S ribosomal gene (V4 region) amplicons using Illumina MiSeq. Data analysis was performed using SAS 9.4, with PROC MIXED used for the mixed model analyses. Results: The analysis characterized mean changes in microbiota diversity over time for both Shannon and Chao indexes. IL6 levels were consistent over time, with an inverse association with Chao but not Shannon index. IL10 and CRP levels changed over time, but without associations with either Shannon or Chao. Pain severity and interference changed over time, but with no associations with inflammatory markers or gut microbiome beta diversity. Fatigue severity and interference changed over time and were positively associated with IL10. Depression did not change over time and was not associated with inflammatory markers or diversity. Conclusions: This study provides preliminary information related to associations between PN symptoms, inflammatory markers, and selected measures of gut microbiome diversity in HCT recipients. Further research is needed to explore and validate these findings to examine the implications for microbiota diversity on inflammatory factors and PN symptoms. Clinical trial information: NCT02398708 .

Exploring and Predicting Landscape Changes and Their Driving Forces within the Mulan River Basin in China from the Perspective of Production–Living–Ecological Space

With rapid economic development and urban expansion, China faces a serious imbalance between production, living, and ecological land use, in which the erosion of water ecological space by urban expansion is especially notable. In order to alleviate or solve this imbalance, this study constructs the water ecological space in the Mulan River Basin based on national land spatial planning using remote sensing statistics and the 2000–2020 statistical yearbooks for the Mulan River Basin. A landscape index is applied to explore this landscape in terms of its production–living–ecological space (PLES) patterns and evolutionary characteristics. Factors affecting the drivers of PLES changes are analyzed through Geo-Detector, and predictions are made using the cellular automata Markov (CA-Markov) model. It was found that (1) PLES distribution patterns in the Mulan River Basin from 2000 to 2020 are dominated by non-watershed ecological spaces, with a significant expansion of living space. Its ecological space is shrinking, and there is significant spatial variation between its near-river and fringe areas. (2) Of the PLES conversions, the most dramatic conversions are those of production space and living space, with 81.14 km2 of production space being transferred into living space. Non-water ecological space and water ecological space are also mainly transferred into production space. (3) As shown by the results of the landscape index calculation, non-water ecological space in the Mulan River Basin is the dominant landscape, the values of the Shannon diversity index (SHDI) and Shannon homogeneity index (SHEI) are small, the overall level of landscape diversity is low, the aggregation index (AI) is high, and the degree of aggregation is obvious. (4) The progressive PLES changes in the Mulan River Basin are influenced by a combination of natural geographic and socioeconomic factors, with the mean population density and mean elevation being the most important factors affecting PLES changes among social and natural factors, respectively. (5) The Kappa coefficient of the CA-Markov model simulation is 0.8187, showing a good simulation accuracy, and it is predicted that the area of water ecological space in the Mulan River Basin will increase by 3.66 km2 by 2030, the area of production space and non-water ecological space will further decrease, and the area of construction land will increase by 260.67 km2. Overall, the aquatic ecological space in the Mulan River Basin has made progress in terms of landscape ecological protection, though it still faces serious erosion. Therefore, attaching importance to the restoration of the water ecological space in the Mulan River Basin, integrating multiple elements of mountains, water, forests, fields, and lakes, optimizing the spatial structure of its PLES dynamics, and formulating a reasonable spatial planning policy are effective means of guaranteeing its ecological and economic sustainable development. This study offers recommendations for and scientific defenses of the logical design of PLES spatial functions in the Mulan River Basin.

Fish biodiversity in modified ecosystems: a case study of Nigeria's Challawa and Tiga dams in the Challawa and Kano rivers

River impoundment is usually accompanied with consequences of alteration in the hydrological system and change in the biodiversity composition of the ecosystem. This study investigated the impact of the dams built on Challawa (that is, Challawa George-Dam) and Kano (that is, Tiga Dam) on the fish biodiversity of the reservoir and below-dam sections of the two rivers. Fish sampling was done using long lines, Malian traps, cast and gill nets from stations on the reservoir and below-dam sections of the rivers. Ten fish species were identified from the reservoir and the below-dam sections of Challawa River belonging to nine families and four orders. Fish communities of the reservoir and below-dam sections of Kano River consisted of 28 species belonging to 12 families and 7 orders. Results of the Shannon diversity index (H^') indicated that the two reservoirs have relatively higher fish species diversity measures (that is, Challawa=1.948 &amp; Kano=2.294) than the below-dam parts (that is, Challawa=1.833 &amp; Kano=2.247) of their respective rivers. Non-metric Multidimensional Scaling (NMDS) analysis produced two-dimensional maps with stress values of 0.0554 and 0.0537, an indication that the model provided good representation of the original data in reduced-dimensional space. The ordination map indicated wide dissimilarities between fish communities of the impounded and below-dam sections. Furthermore, a one-way analysis of similarity indicated significant difference (P=0.0001) and high dissimilarities (R=0.643) between fish communities in the two sections of Challawa River and also in Kano River (P=0.001, R=0.929). Analysis of Similarity Percentage indicated 74.45% of the dissmilarities between fish communities in the two sections were cummulatively contributed by four species in Challawa River and 72.18% by five species in Kano River. The distinct differences in fish abundance and richness between the two sections is ascribed to increased ecosytem productivity often associated with the inundated portion of dammed river. It is recommended that more water flow across the dams should be encouraged as a mitigating measure to boost basin sizes of the rivers at the below-dam sections. Key words: Diversity, dam, impound, reservoir, community, freshwater and fish species

Socio-Economic Drivers of Agroforestry Practices in Kaiti Watershed, Makueni County, Kenya

Forests and trees are essential resources for sustainable provision of goods and services. However, trees have not only been depleted in reserved forests but also on agricultural lands. Several measures have been formulated to improve forest cover in Kenya and one of such strategies is agroforestry. This study aimed to examine agroforestry practices, tree density on farms and determine the relationship between socio-economic characteristics of households and tree density on farms in Kaiti watershed, Makueni County, Kenya. Quadrats were used to determine tree density and tree species diversity on farms while questionnaires were used to record socio-economic characteristics of households. Data files were prepared in the Microsoft Excel and SPSS version 20 software where descriptive and inferential statistics were used. The study found 8 agroforestry practices. The results of One-Way ANOVA for both Shannon Diversity Index and Simpsons’ Index of Diversity showed significant difference in species diversity in Kaiti watershed with p-value of 0.00023 and 0.00012, respectively. The mean of tree density was 104.5 trees per acre where 54% of farms had less than 40 trees per acre while 46% of farms had more than 40 trees per acre. Further, the study found significant relationship between socio-economic characteristics of households and tree density on farms. Household income was the most significant with p-value of 0.000. The study recommends sensitization of farmers about importance of trees and suitable tree species for growing in arid and semi-arid areas. Further, supply of certified seedlings close to farmers and at affordable prices would improve tree species diversity and tree density on farms. There is also need for private land ownership for households to promote sense of ownership of trees

The impact of Ethiopian Green Legacy Initiative (GLI) on landscape functionality and plant species diversity in Lake Hawassa watershed, Ethiopia

AbstractAs one of the responses to the global commitments against climate change, the Ethiopian Government launched a nationwide Green Legacy Initiative (GLI) in 2019, which largely focused on forest tree plantations with some inclusion of fruit trees. Despite its tremendous efforts and investments, its effectiveness and impacts have not been studied. This paper attempted to address this necessity by conducting a cross‐sectional quasi‐experiment in three randomly selected woredas/districts of Lake Hawassa Watershed from August 20 to September 2, 2023. The research hypothesized the likely impacts of GLI on four dependent variables (hydrological regulation, soil stability, nutrient cycling and plant species diversity). To achieve this, the research considered the two variants of GLI practices (plantation with and without soil and water conservation measures) and the corresponding control sites. Having three sites and three treatments with five replications, the study involved a total of forty‐five quadrats of the same size (20 m × 20 m). The first three parameters were analysed using the landscape functionality analysis method, while the fourth employed Shannon's diversity index. Results of ANOVA showed that, on average 87% of randomly selected quadrats were found to significantly improve the local hydrology (runoff potential) (≈ 83.3% with Av. p = 0.012), soil stability (≈100% with Av. p = 0.002), nutrient cycling (≈83.3% with Av. p = 0.017) and plant species diversity (≈83.3% with Av. p = 0.012). The research revealed positive results from the Ethiopian Green Legacy Initiative. The small number of samples is acknowledged as a limitation of the research.

Short communication: Comparing the microbiota diversity from the core, middle part and rind of six Spanish commercial goat cheeses

The cheese core has a lower oxygen saturation and salinity and a higher acidity than the rind, but there is controversy about the incidence of such factors on the magnitude of microbial diversity. The goal of the current work was to investigate the existence of differences in α-diversity between the core, middle part, and rind of six Spanish commercial cheeses through a sequencing approach. To this end, we have collected rind, middle part, and core samples from fresh (H and M), soft semi-ripened (C and P), hard semi-ripened (B) and semi-hard aged (G) goat cheeses. After purifying deoxyribonucleic acid from these 18 samples, the V3-V4 ultravariable region of the 16S rRNA gene was sequenced. The analysis of microbial composition revealed that lactic acid bacteria from the genera Lactococcus, Lactobacillus, Streptococcus, and Leuconostoc are predominant in all six goat cheeses. Furthermore, we identified several psychrophilic taxa often associated with the post-pasteurization contamination of refrigerated milk. Comparison of three α-diversity estimators (Chao1, Shannon and Faith's phylogenetic diversity indices) of microbiota in the core, middle part, and rind of all six goat cheeses did not reveal substantial differences, being only significant (at the nominal level) the comparison of rind vs middle part for the Shannon index (P-value = 0.031). Moreover, the construction of a dendrogram based on Aitchison distances revealed that cheese samples cluster according to their manufacturing characteristics, with a clear distinction between fresh vs semi-ripened or aged cheeses. We conclude that the magnitude of microbial α-diversity in the cheese core is similar to that in the rind despite their different physicochemical attributes. This result could be because physicochemical differences between cheese compartments are often attenuated during cheese ripening.

#983 Identification of gut microbiome signatures associated with albuminuria in diabetes mellitus

Abstract Background and Aims Diabetes is a growing global problem with serious complications, including kidney impairment and cardiovascular morbidity and mortality. Monitoring albuminuria, which is associated with these complications, is crucial in optimal diabetes management. Recent research suggests a link between the gut microbiome, plasma metabolites and albuminuria development in diabetes patients, highlighting the need for further investigation using deep metagenomic sequencing. Method We investigated the relationship between 1002 gut microbial species, 1308 metabolites and albuminuria in 752 participants with diabetes from the Swedish CArdioPulmonary BioImage Study. To determine the relative abundance of species, we employed deep shotgun metagenomic sequencing of fecal samples. Plasma metabolites were analyzed using mass spectrometry-based methods. Results Shannon diversity index was inversely associated with albuminuria after adjusting for confounding factors (Fig. 1). Our multivariable-adjusted models revealed seven metagenomic species that were associated with albuminuria (Fig. 2). Furthermore, employing a global metabolomics approach, we identified phenyl sulfate, among 98 annotated metabolites (Fig. 3), as linked to the species Clostridium sp. AT4 and Eggerthella lenta. Notably, phenyl sulfate is involved in tyrosine metabolism, and we also observed an association between the gut metabolic module of Tyrosine degradation II and albuminuria. Conclusion In the present study, we identified seven gut microbial species linked to albuminuria and established a connection between these species and phenyl sulfate, which previously has been associated with podocyte damage and the development of albuminuria. These findings provided additional evidence of the impact of microbial species and contribute to our understanding of the complex relationship between the gut microbiome, plasma metabolites, and albuminuria in patients with diabetes.

Insights into the Correlation between Microbial Community Succession and Pericarp Degradation during Pepper (Piper nigrum L.) Peeling Process via Retting.

White pepper, used both as a seasoning in people's daily diets and as a medicinal herb, is typically produced by removing the pericarp of green pepper through the retting process. However, the mechanism of the retting process for peeling remains unclear. Therefore, this study aimed to investigate the changes in physicochemical factors, microbial community succession effects, and metabolites of the pepper pericarp during the pepper peeling process. The findings indicated that pre-treatment involving physical friction before the retting process effectively reduced the production time of white pepper. During the retting process, the pectinase activity increased, leading to a decrease in the pectin content in the pepper pericarp. There was a significant correlation observed between the changes in pH, pectin content, and peeling rate and the Shannon diversity index of bacteria and fungi. Prevotella, Lactococcus, and Candida were the dominant microbial genera during the retting. The functional predictions suggested that the monosaccharides degraded from the pepper pericarp could have been utilized by microbes through sugar metabolism pathways. Metabolomic analysis showed that the metabolic pathways of carbohydrates and amino acids were the main pathways altered during the pepper peeling process. The verification experiment demonstrated that the degradation of pectin into galacturonic acid by polygalacturonase was identified as the key enzyme in shortening the pepper peeling time. The structure of the pepper pericarp collapsed after losing the support of pectin, as revealed by scanning electron microscopy. These results suggest that the decomposition of the pepper pericarp was driven by key microbiota. The succession of microbial communities was influenced by the metabolites of the pepper pericarp during retting. These findings provide new insights into the retting process and serve as an important reference for the industrial production of white pepper.

Carbohydrate structural complexity modulates the formation, composition and functionality of microbial flocs and its impact on gut microbiota and growth of Pacific white shrimp

The addition of carbohydrate into the culture water to facilitate the growth of heterotrophic bacteria is a common practice in shrimp grow out culture. The present study aimed to evaluate the effect of carbohydrate structural complexity on the formation, composition and functionality of microbial flocs, and how it impacts the gut microbiome and growth of Pacific white shrimp (Litopenaeus vannamei). Pacific white shrimp juveniles (1.07 ± 0.01 g) were randomly distributed in 12 indoor fiber tanks (50 cm × 50 cm × 100 cm) and maintained for 30 days at stocking density 107 ind.m−3 (20 ind per tank). Three different carbohydrate sources were added according to the treatments, that is dextrose (Dx) representing simple carbohydrate, potato starch (St) representing starch polysaccharide, and cellulose (Cl) representing complex non-starch polysaccharide. Settleable solids level and particle size of microbial flocs in Dx treatment were consistently higher than those of St and Cl treatments (P < 0.05). Amino acids concentrations were not significantly different amongst the treatments (P > 0.05), however essential amino acid index relative to shrimp requirement was the lowest in the Dx treatment (P < 0.05). Shannon diversity index level in the microbial flocs with Cl as the carbohydrate sources was higher compared to Dx and St. T6SS2 and ExsA gene expressions in the co-culture of Vibrio parahaemolyticus and the microbial floc suspension was highly upregulated in Dx treatment. Accordingly, differences in the shrimp gut microbiome was also observed amongst the treatments. The highest growth performance was demonstrated by the shrimp cultured with cellulose as the carbohydrate source. In conclusion, carbohydrate structural complexity could significantly affect the characteristics of microbial flocs suspended in the culture water and could ultimately affect the shrimp growth performance.

A landscape index for indicating the spatio-temporal dynamics of carbon storage in an opencast coal mine

Coal is China’s main resource, with open-pit mining accounting for a significant portion of global production. However, this activity, including mining and ecological restoration, can have a definite impact on ecosystem carbon storage and its distribution; its associated factors are also unclear. In this paper, we quantify the carbon storage changes in Haerwusu coal mine, a typical large-scale coal mine in China, based on land use/land cover (LULC) characteristics, and analyze the impact factors of carbon density from 2007 to 2022 by integrating the InVEST model with the landscape ecological function contribution ratio and multiple regression model. The results are as follows. (1) Carbon storage decreased from 159.95 × 104 to 147.51 × 104 from 2007 to 2017 and then increased to 151.91 × 104 to 2022. (2) The degree of coordination between carbon storage forest and grassland area landscape pattern coupling ranged from 0.887 to 0.867 from 2007 to 2022, with the lowest point at 0.720 in 2012. (3) Carbon storage was significantly related to vegetation indices, temperature, and elevation, and these factors can explain 37.5% of the carbon storage spatial variability; stepwise regression analysis showed that the integration of landscape patterns, such as Shannon’s diversity index (SHEI) and the aggregation index (AI), could improve the explanation by 1.4%. (4) Based on the analysis of the landscape ecological function contribution ratio, the carbon storage-sensitive areas can be classified into three levels: extremely sensitive areas ranging 0 to 4 km from the mine, sensitive areas ranging 4 to 8 km, and insensitive areas ranging beyond 8 km. This study proposes a strategy for analyzing changes of carbon storage in coal mines, highlights the important role of landscape patterns in influencing carbon storage, and provides a reliable reference support for the ecological management of coal mines.

Landscapes with higher crop diversity have lower aphid species richness but higher plant virus prevalence

Abstract Diversifying agricultural systems by growing more than one crop species in an area can decrease pest and disease pressure and increase crop yields. However, there is a lack of information on how crop diversity at larger spatial scales influences pest and disease pressure. Here, we investigated how landscape‐scale crop diversity affects aphid vector communities and prevalence of non‐persistently transmitted potato virus Y (PVY). To test the influence of landscape‐scale crop diversity on PVY prevalence and aphid communities, we conducted a field study during the 2020 and 2021 field seasons in the San Luis Valley, Colorado, where we quantified aphid communities and PVY incidence at multiple sites. We then determined the association between aphid species richness and abundance and PVY incidence with landscape variables (crop diversity metrics and percentage cover of crop species) within 1, 2 and 3 km buffers from study sites. Higher crop diversity (measured as Shannon Diversity Index) led to decreased aphid species richness at a 3 km buffer in the 2021 field season. We only detected a positive association between percentage of alfalfa crop cover and aphid species richness in 2020 and aphid abundance in 2021 within a 1 km buffer. Higher crop diversity led to increased PVY incidence at a 2 km buffer in 2021 and 3 km buffer in 2020 and 2021. At a 3 km buffer in 2021, we found a positive influence of crop species richness on PVY incidence and a negative influence of crop species evenness on PVY incidence. Also in 2021, we found a positive influence of percentage of potato (virus host) on PVY incidence and a negative influence of percentage of barley (virus non‐host) on PVY incidence. Synthesis and applications. In summary, we found that landscape‐scale crop diversity impacts plant virus prevalence at spatial scales of &gt;1 km. This suggests that potato growers could reduce PVY prevalence by geographically isolating potato fields from other potato or other PVY hosts. Crop diversity had a negative influence on aphid vector communities, so growers could reduce risk of virus spread by aphid vectors by using certified potato seed in a diversified landscape.

Relationship between Landscape Pattern and Human Disturbance in Serbia from 2000 to 2018

This study intends to verify how the alteration of the landscape configuration, represented by different metrics of configuration and diversity, is related to the intensity of human disturbance. The objectives of the study are: (1) to quantify the change in land use/land cover (LULC) patterns and the degree of human disturbance in Serbia between 2000 and 2018, and (2) to study the relationship between LULC configuration and the impact resulting from human disturbance under different levels of intensity, to understand how changing trends in landscape pattern can serve as indicators to estimate landscape changes resulting from human actions. The Hemeroby Index (HI) was calculated to quantify the impacts on ecosystems resulting from disturbance caused by human actions. Based on the analysis of the variation in the value corresponding to the HI for the period between 2000 and 2018, the level of naturalness increased by only 5% of the territory of Serbia, with this change being verified mainly in SE Serbia. The landscape pattern was quantified using a set of LULC metrics. We used the Spearman method to identify the existing statistical correlations between the geometric parameters of the landscape and the HIs values. At the landscape level, the Mean Shape Index, Edge Density, Mean Patch Fractal Dimension, and Shannon Diversity Index show a strong negative correlation with HI. This correlation suggests that landscapes with greater structural complexity are good indicators of low levels of hemeroby. At the class level, Edge Density and Mean Patch Size correlate significantly with the HI for artificial surfaces, agricultural areas, forests, and semi-natural areas.

Association among polydisperse aerodynamic size of bioaerosols, biodiversity and urbanization in kindergartens

The aerodynamic sizes of bioaerosols may significantly affect their behaviors, respiratory deposition and biodiversity. The respirable bacterial size, biodiversity, and human-associated bacteria (HAB) related bioaerosols were evaluated at three kindergartens in Taiwan. Kindergartens A, B, and C were in urban, semi-urban, and rural areas, respectively. A six-stage viable Andersen cascade impactor was used to collect bioaerosols and to determine their size distributions. The geometric mean diameter (GMD), geometric standard deviation (GSD), heat maps, and uniformity were used to evaluate the association of bacteria characteristics. A BD Phoenix-100 automated interpretation system was used to identify the airborne bacteria species.The results revealed that 1425 colonies of the sampled airborne bacteria contained 63 species in 29 genera, and overall, 63.0% were HABs. The most abundant phylum was Actinobacteria (56.6 ± 22.2%) and Firmicutes (31.6 ± 22.3%), and from the taxonomic analysis, both airborne Micrococcus and the Staphylococcus aureus are the dominant genus. All the bacteria aerodynamic particle size distributions were polydisperse distributions. The heat map and uniformity analysis had revealed most of the sampled bioaerosols distributed between 1.1–3.3 μm, and most of the polydisperse airborne Streptococcus spp. had a size in the respirable range, due to urbanization, they have potentially contributed to respiratory risk in the kindergartens. The Shannon diversity index (H) and inverse Simpson diversity index (D) of the bioaerosols in urban kindergarten were negatively correlated with GMD and GSD. The Pearson correlations revealed that the kindergarten in the rural area, with a higher temperature, a lower relative humidity, and a lower CO2 concentration than the others, tended to have the largest H and D values (P < 0.05). Multiple and stepwise regression revealed that bioaerosol aerodynamic size was statistically significantly correlated with H (P = 0.001) and D values (P = 0.002). This study sheds light on the characteristics of bioaerosols and their associations with microbiome.