Statistical challenges in longitudinal microbiome data analysis.

The microbiome is a complex and dynamic community of microorganisms that co-exist interdependently within an ecosystem, and interact with its host or environment. Longitudinal studies can capture temporal variation within the microbiome to gain mechanistic insights into microbial systems; however, current statistical methods are limited due to the complex and inherent features of the data. We have identified three analytical objectives in longitudinal microbial studies: (1) differential abundance over time and between sample groups, demographic factors or clinical variables of interest; (2) clustering of microorganisms evolving concomitantly across time and (3) network modelling to identify temporal relationships between microorganisms. This review explores the strengths and limitations of current methods to fulfill these objectives, compares different methods in simulation and case studies for objectives (1) and (2), and highlights opportunities for further methodological developments. R tutorials are provided to reproduce the analyses conducted in this review.

Gut microbiome in diabetic retinopathy: A systematic review and meta-analysis.

CONTEXT: Changes in the gut microbiome are linked with Type 2diabetes mellitus (T2DM) development, but alterations in patients with diabetic retinopathy (DR) are still being debated. OBJECTIVE: To investigate the differences in biodiversity and relative abundance of gut microbiome between patients with DR and T2DM. METHODS: A comprehensive search was performed in five electronic databases (PubMed, EMBASE, Cochrane Central Register of Controlled Trials, Web of Science, and CNKI) from the inception of each database through to August 2023. The standardized mean difference (SMD) and its 95% confidence interval (CI) were estimated using Stata 15.1. Furthermore, the alpha diversity index and relative abundance of the gut microbiome were calculated. The Egger test determined publication bias in the literature. RESULTS: Seven case-control studies were included in the final dataset, comprising 195 patients with DR and 211 patients with T2DM. Compared to T2DM patients, patients in the DR group had a reduced but not significantly different α-diversity. The analysis of microbial composition at the phylum level revealed a marked increase in the relative abundance of Bacteroidetes(ES = 23.27, 95%CI[8.30, 38.23], P = 0.000) and a decline in Firmicutes(ES = 47.05, 95%CI[36.58, 57.52], P = 0.000), Proteobacteria (ES = 11.08, 95%CI[6.08, 16.07], P = 0.000) and Actinobacteria (ES = 10.43, 95%CI[1.64, 19.22], P = 0.001) in patients with DR when compared to those with T2DM. CONCLUSIONS: An association exists between alterations in the gut microbiome of T2DM and the development and progression of DR. This suggests that re-establishing homeostasis of the gut microbiome could be a potential way to prevent or treat DR and requires further confirmation in future studies. REGISTRATION DATABASE: Prospero. REGISTRATION NUMBER: CRD42023455280.

Foliar phenols and flavonoids level in pteridophytes: an insight to culturable fungal endophyte colonisation.

There are many available reports of secondary metabolites as bioactive molecules from culturable endophytes, nevertheless, there are scarce research pertaining to the levels of metabolites in plants with respect to the incidence and colonisation of fungal endophytes in the same foliar tissues. Therefore, the study was focussed to examine whether fungal endophyte colonisation and the accumulation of secondary metabolites, such as flavonoids and phenols, in the plants are related in any way. For this reason, the study aims to analyse phenols and flavonoids from the fronds of eleven pteridophytes along with the culture-dependent isolation of fungal endophytes from the host plants subsequently assigning them to morphological category and their quantitative analysis and further resolving its identities through molecular affiliation. The results revealed that nine morpho-categories of fungal endophytes were allotted based on culture attributes, hyphal patterns and reproductive structural characters. Highest numbers of species were isolated from Adiantum capillus-veneris and least was recorded from Pteris vittata and Dicranopteris linearis. Maximum phenol content was analysed from the fronds of P. vittata and lowest was recorded in A. capillus-veneris. Highest flavonoid content was measured in D. linearis and lowest was detected in Christella dentata. Significant negative correlation was observed between phenol content of ferns and species richness of fungi. Moreover, significant positive correlation was observed with the relative abundance of Chaetomium globosum and flavonoid content of ferns and negative significant relation was found between relative abundance of Pseudopestalotiopsis chinensis and phenol content of pteridophytes. The occurrence and the quantitative aspects of endophytes in ferns and their secondary metabolites are discussed.

Local and regional-scale effects of hedgerows on grassland- and forest-associated bird populations within agroecosystems.

Linear woody features (LWFs), like hedgerows along field edges, provide wildlife habitat and support biodiversity in agroecosystems. Assessments of LWFs usually focus on community-level indices, such as species richness. However, effective conservation actions need to balance the contrasting habitat preferences of different wildlife species, necessitating a focus on population-level effects in working landscapes. We assessed associations between LWFs and abundance for 45 bird species within an intensive agroecosystem in eastern Ontario, Canada. We used distance- and removal-sampling methods across 4 years (2016-2019) to estimate local bird abundance in habitats representing a range of LWF densities. We also predicted abundance across a subset of the study region with and without LWFs to understand their contribution to regional population density. Associations between local bird abundance and LWFs were variable among species, but overall community effects were clearly positive, particularly for forest and shrubland species. At the site level, 20/45 species (44%) had higher densities associated with greater LWF presence on average, compared to 5/45 (11%) with negative associations. At the regional scale, LWFs had predicted benefits on total abundance for 31 species (69%), contributing to an estimated 20% increase on average. Positive effects were most pronounced in areas with greater agricultural land use (primarily field crops), suggesting LWFs may provide crucial habitat in heavily modified landscapes but have little to no additional benefit for the avian community in areas with greater existing heterogeneity and habitat retention. Species that responded negatively tended to be at risk with strong habitat preferences for intact forests or large, open grasslands and, thus, greater sensitivity to potential edge effects. With rapidly declining songbird populations and a global need for food security, conservation strategies that amplify biodiversity and enhance agricultural productivity through ecosystem services such as pest control, pollination, and water regulation are vital. We demonstrate the benefits of habitat heterogeneity in agroecosystems on songbird densities and highlight the need to integrate local and landscape-level assessments in conservation planning. An effective, balanced strategy includes concentrating LWFs in areas of extensive arable crops, with habitat retention patches where possible, while maintaining heterogeneity through mixtures of natural habitats and pastoral farming in less intensive regions.

Les caractéristiques d'emboisement linéaires (CEL), tels que les haies en bordure de champs, fournissent un habitat à la faune et à la flore et favorisent la biodiversité dans les agroécosystèmes. Les évaluations des caractéristiques d'emboisement linéaires se concentrent généralement sur des indices au niveau de la communauté, tels que la richesse des espèces. Cependant, pour être efficaces, les actions de conservation doivent équilibrer les préférences variables des différentes espèces sauvages en matière d'habitat, ce qui nécessite de se concentrer sur les effets au niveau de la population dans les paysages exploités. Nous avons évalué les associations entre les CEL et l'abondance de 45 espèces d'oiseaux dans un agroécosystème intensif de l'est de l'Ontario, au Canada. Nous avons utilisé des méthodes d'échantillonnage par distance et par enlèvement sur quatre ans (2016­2019) pour estimer l'abondance locale des oiseaux dans des habitats représentant une gamme de densités de CEL. Nous avons également prédit l'abondance dans un sous­ensemble de la région étudiée avec et sans CEL pour comprendre leur contribution à la densité de la population régionale. Les associations entre l'abondance des oiseaux locaux et les CEL étaient variables d'une espèce à l'autre, mais les effets globaux sur les communautés étaient clairement positifs, en particulier pour les espèces des forêts et des zones arbustives. Au niveau du site, 20/45 espèces (44%) avaient des densités plus élevées associées à une plus grande présence de CEL en moyenne, contre 5/45 (11%) avec des associations négatives. À l'échelle régionale, les CEL ont eu des effets bénéfiques sur l'abondance totale de 31 espèces (69%), contribuant à une augmentation estimée à 20% en moyenne. Les effets positifs étaient plus prononcés dans les zones où l'utilisation des terres agricoles était plus importante (principalement les grandes cultures), ce qui suggère que les CEL peuvent fournir un habitat crucial dans les paysages fortement modifiés, mais qu'elles ont peu ou pas d'avantages supplémentaires pour la communauté aviaire dans les zones où l'hétérogénéité existante et la conservation de l'habitat sont plus importantes. Les espèces qui ont répondu négativement avaient tendance à être en danger, avec de fortes préférences d'habitat pour les forêts intactes ou les grandes prairies ouvertes, et donc une plus grande sensibilité aux effets de lisière potentiels. Avec le déclin rapide des populations d'oiseaux chanteurs et le besoin mondial de sécurité alimentaire, les stratégies de conservation qui amplifient la biodiversité et améliorent la productivité agricole grâce aux services écosystémiques tels que la lutte contre les ravageurs, la pollinisation et la régulation de l'eau sont vitales. Nous démontrons les avantages de l'hétérogénéité de l'habitat dans les agroécosystèmes sur les densités de passereaux et soulignons la nécessité d'intégrer les évaluations locales et au niveau du paysage dans la planification de la conservation. Une stratégie efficace et équilibrée consiste à concentrer les CEL dans les zones de cultures arables extensives, avec des parcelles de conservation de l'habitat là où c'est possible, tout en maintenant l'hétérogénéité grâce à des mélanges d'habitats naturels et à l'agriculture pastorale dans les régions moins intensives.

Premodulator microbiome alterations associated with postmodulator growth outcomes in pediatric cystic fibrosis: Can we predict outcomes?

OBJECTIVES: The gut microbiota plays an important role in childhood growth. Our longitudinal cohort includes children with children with cystic fibrosis (CwCF) treated with highly effective modulator therapy. We aimed to elucidate early premodulator microbial signatures associated with postmodulator weight for CwCF later in childhood. METHODS: Stool samples were collected from CwCF at 13 days to 60 months. Metagenomic sequencing determined differentially abundant taxa. Children with body mass index or weight for length Z-scores within 1 standard deviation of the mean (SD) were considered normal weight, those >1 SD were classified as risk of overweight while children <1 SD were considered undernourished, although no CwCF met this latter criterion here. Multivariate regression models were applied to identify significant associations between metadata and microbial taxonomic relative abundances. RESULTS: One hundred and eighty-nine stool samples were analyzed from 39 CwCF. We identified statistically significant differences in early microbiome patterns among those at risk of being overweight compared to those who were normal weight when adjusted for age, sex, CF mutation, and early feeding method. Early microbiome was a stronger driver of growth status than current modulator use. Among those at risk of overweight, several taxa that were consistently in lower abundance included Eggerthella lentha, Ruminococcus, Bacteroides, with increase in abundance of Bacteroides stercoris. CONCLUSIONS: The early microbiome strongly predicts growth in the setting of modulator use for CwCF and we identify microbiome signatures associated with risk of being overweight. We highlight the possibility for interventions or early alternations to nutritional guidance for prevention of comorbid complications.

Effects of atrazine on movement, metabolism and gene expression in Pelophylax nigromaculatus larvae under global warming.

Global warming and environmental pollutants both pose a threat to the behavior and physiology of animals, but research on the combined effects of the two is limited. Atrazine, a widely used herbicide, has toxic effects on organisms. In this study, the effects of environmental concentrations of atrazine exposure (100 µg/L) for seven days on the movement, metabolism and gene expression related to motility of Pelophylax nigromaculatus larvae (GS8) were investigated under global warming. The results showed that compared to the optimal growth temperature (18 °C), atrazine treatment under global warming (21 °C) significantly increased the average speed (about 11.2 times) and maximum acceleration (about 1.98 times) of P. nigromaculatus larvae, altered the relative abundance of 539 metabolites, including Formyl-5-hydroxykynurenamine, 2,4-Dihydroxybenzophenone, and FAPy-adenine, and changed the nucleotide metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and purine metabolism, as well as increased the gene expression of SPLA2 (about 6.46 times) and CHK (about 3.25 times). In summary, atrazine treatment under global warming caused metabolic disorders in amphibian larvae and increased the expression of some movement-related genes in the brain, resulting in abnormally active.

Gut microbiome is associated with asthma and race in children with food allergy.

BACKGROUND: The composition of the gut microbiome has been associated with development of atopic conditions such as food allergy (FA) and asthma. African American or Black children with FA have higher rate of asthma compared to their White counterparts. OBJECTIVE: We sought to investigate whether the diversity and relative abundance (RA) of gut microbiota is different between children with FA from different racial backgrounds living in the same cities. Furthermore, we aimed to understand whether the difference in the gut microbiota is associated with asthma in children with FA. METHODS: We analyzed and compared the stool microbiome of a cohort of Black and White children with FA by shotgun genomic sequencing. RESULTS: A total of 152 children with IgE-mediated FA enrolled onto FORWARD (Food Allergy Outcomes Related to White and African American Racial Differences); 30 Black and 122 White children were included. The RA of several bacteria was associated with race and asthma. Most notably the RA of Bacteroides thetaiotaomicron, Chlamydia thrachomatis, Parabacteroides goldsteinii, and Bacteroides eggerthii were significantly higher, while the RA of Bifidobacterium sp CAG:754, Parabacterium johnsonii, Bacteroides intestinalis, and Bifidobacterium breve were significantly lower in stool samples of Black children compared to White children. Asthma was associated with lower RA of B breve, Bifidobacterium catenulatum, Prevotella copri, Veilloella sp CAG:933, and Bacteroides plebius, and higher RA of 3 Bacteroides species. CONCLUSIONS: The observed variations in the gut microbiota of Black and White children such as differences in the Bacteroides and Bifidobacterium species along with their association to history of asthma in our cohort is indicative of their potential role in the higher rate of asthma observed among Black children with FA.

New insights into the origin of buckwheat cultivation in southwestern China from pollen data.

Buckwheat is an important crop which originated in China and spread widely across Eurasia. However, exactly where in China domestication took place remains controversial. Archaeological and palynological records suggest a longer cultivation history of buckwheat in northern China than in southwestern China, but this conflicts with phylogenetic evidence implicating southwestern China as the centre of origin and diversity of buckwheat. We investigate alternative methodologies for inferring the occurrence of buckwheat cultivation and suggest that relative abundance could provide a reliable measure for distinguishing between wild and cultivated buckwheat in both present-day and fossil samples. Approximately 12 800-yr palaeoecological record shows that Fagopyrum pollen occurred only infrequently before the early Holocene. As southwestern China entered the early agricultural period, c. 8000-7000 yr ago, a slight increase in abundance of Fagopyrum pollen was observed. Approximately 4000 yr ago, concurrent with the Pu minority beginning to develop dry-land agriculture, the abundance of Fagopyrum pollen increased significantly, suggesting the cultivation of this crop. Fagopyrum pollen rose to a maximum value c. 1270 yr ago, suggesting an intensification of agricultural activity. These findings fill a gap in the Fagopyrum pollen record in southwestern China and provide new indications that early cultivation may have occurred in this region.

Gut microbiome characteristics in subjective cognitive decline, mild cognitive impairment and Alzheimer's disease: a systematic review and meta-analysis.

BACKGROUND AND PURPOSE: The gut microbiome has been reported to be closely related to Alzheimer's disease (AD) progression. Here, a comprehensive meta-analysis of gut microbial characteristics in AD, mild cognitive impairment (MCI) and subjective cognitive decline (SCD) was performed to compare gut microbial alterations at each stage. METHODS: A total of 10 databases (CNKI, WanFang, VIP, SinoMed, WOS, PubMed, Embase, Cochrane Library, PsycINFO and Void) were searched and 34 case-control studies were included. α and ß diversity and the relative abundance of gut microbiota were analysed as outcome indices. Data analysis was performed using Review Manager (5.4.1) and R. RESULTS: Chao1 and Shannon index levels in AD were significantly lower compared with healthy controls (HCs), and the Chao1 index was significantly lower in MCI compared with HCs. There was a significant difference in ß diversity of gut microbiomes in patients (SCD, MCI, AD) compared with HCs. The relative abundance of Firmicutes at the phylum level was significantly lower in patients with AD and MCI than HCs. However, the relative abundance of Bacteroidetes at the phylum level was significantly higher in patients with MCI than HCs. There was an increasing trend for Enterobacteriaceae and a decreasing trend for Ruminococcaceae, Lachnospiraceae and Lactobacillus during AD; Lactobacillus showed a decreasing trend early in SCD. CONCLUSION: Our results indicated that there were gut microbiological abnormalities in AD, even as early as the SCD stage. The dynamic, consistent changes in gut microbes with the disease process showed that they might serve as potential biomarkers for early identification and diagnosis of AD.

Planktonic microbial community and biological metabolism in a subtropical drinking water river-reservoir system.

To understand the dynamics of planktonic microbial community and its metabolism processes in subtropical drinking water river-reservoir system with lower man-made pollution loading, this study selected Dongzhen river-reservoir system in Mulan Creek as object to investigate spatial-temporal characteristics of community profile and functional genes involved in biological metabolism, and to analyze the influence of environmental factors. The results indicated that Proteobacteria and Actinobacteria were the most diverse phyla with proportion ranges of 9%-80% in target system, and carbohydrate metabolism (5.76-7.12 × 10-2), amino acid metabolism (5.78-7.21 × 10-2) and energy metabolism (4.07-5.17 × 10-2) were found to be the dominant pathways of biological metabolism. Although there were variations in biological properties both spatially and temporally, seasonal variation had a greater influence on microbial community and biological metabolism, than locational differences. Regarding the role of environmental factors, this study revealed that microbial diversity could be affected by multiple abiotic factors, with total organic carbon, total phosphorus and temperature being more influential (absolute value of standardized regression weights >2.13). Stochastic processes dominated the microbial community assembly (R2 of neutral community model = 0.645), while niche-based processes differences represented by nutrients, temperature and pH level played secondary roles (R > 0.388, P < 0.01). Notably, the synergistic influences among the environmental factors accounted for the higher percentages of community variation (maximum proportion up to 17.6%). Additionally, pH level, temperature, and concentrations of dissolved oxygen, carbon and nitrogen were found to be the significant factors affecting carbon metabolism pathways (P < 0.05), yet only total organic carbon significantly affected on nitrogen transformation (P < 0.05). In summary, the microbial profile in reservoir is not completely dominated by that in feeding river, and planktonic microbial community and its metabolism in subtropical drinking water river-reservoir system are shaped by multiple abiotic and biotic factors with underlying interactions.

Age-Related Cognitive Decline, Focus on Microbiome: A Systematic Review and Meta-Analysis.

Aging is a complex process influenced by genetics and the environment, leading to physiological decline and increased susceptibility to diseases. Cognitive decline is a prominent feature of aging, with implications for different neurodegenerative disorders. The gut microbiome has gained attention for its potential impact on health and disease, including cognitive function. This systematic review and meta-analysis aimed to investigate the relationship between the gut microbiome and cognitive function in the context of aging. Following PRISMA guidelines, a comprehensive search strategy was employed in PubMed, Scopus, and Web of Science databases. Studies exploring the role of the microbiome in cognition and neurodegenerative disorders, published between 2013 and 2023, were included. Data extraction and quality assessment were performed. Quantitative synthesis using statistical analyses was performed to examine microbial diversity and relative abundance in various cognitive conditions. Sixteen studies involving a total of 1303 participants were included in the analysis. The gut microbiota's relative abundance was different in individuals with cognitive impairments such as Alzheimer's disease, Parkinson's disease, and dementia, compared to the healthy controls. The most prevalent phyla affected were Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Meta-analyses indicated substantial heterogeneity among studies focusing on Alzheimer's disease. The overall quality of evidence related to microbial analysis was moderate. The gut microbiome's role in cognitive decline and neurodegenerative disorders warrants investigation. Altered microbial abundance, particularly in specific phyla, is associated with cognitive impairments. However, variations in study findings and methodologies highlight the complexity of the relationship between the gut microbiome and cognitive function. Further studies are needed to better understand the mechanisms underlying this connection and its potential implications for aging and cognitive health.

Structural and compositional segregation of the gut microbiota in HCV and liver cirrhotic patients: A clinical pilot study.

Gut microbial dysbiosis during the development of Hepatitis C virus and liver-related diseases is not well studied. Nowadays, HCV and liver cirrhosis are the major concerns that cause gut bacterial alteration, which leads to dysbiosis. For this purpose, the present study was aimed at correlating the gut bacterial community of the control group in comparison to HCV and liver cirrhotic patients. A total of 23 stool samples were collected, including control (9), liver cirrhotic (8), and HCV (6). The collected samples were subjected to 16 S rRNA Illumina gene sequencing. In comparison with control, a significant gut bacterial alteration was observed in the progression of HCV and liver cirrhosis. Overall, Firmicutes were significantly abundant in the whole study. No significant difference was observed in the alpha diversity of the control and patient studies. Additionally, the beta diversity based on non-metric multidimensional scaling (NMDS) has a significant difference (p = 0.005) (ANOSIM R2 = 0.14) in all groups. The discriminative results based on the LEfSe tool revealed that the HCV-infected patients had higher Enterobacteriaceae and Enterobacterial, as well as Lactobacillus and Bacilli in comparison than the liver-cirrhotic patients. These taxa were significantly different from the control group (p < 0.05). Regarding prospects, a detailed analysis of the function through metagenomics and transcriptomics is needed.

Subsurface Manure Injection Reduces Surface Transport of Antibiotic Resistance Genes but May Create Antibiotic Resistance Hotspots in Soils.

Compared to surface application, manure subsurface injection reduces surface runoff of nutrients, antibiotic resistant microorganisms, and emerging contaminants. Less is known regarding the impact of both manure application methods on surface transport of antibiotic resistance genes (ARGs) in manure-amended fields. We applied liquid dairy manure to field plots by surface application and subsurface injection and simulated rainfall on the first or seventh day following application. The ARG richness, relative abundance (normalized to 16s rRNA), and ARG profiles in soil and surface runoff were monitored using shotgun metagenomic sequencing. Within 1 day of manure application, compared to unamended soils, soils treated with manure had 32.5-70.5% greater ARG richness and higher relative abundances of sulfonamide (6.5-129%) and tetracycline (752-3766%) resistance genes (p ≤ 0.05). On day 7, soil ARG profiles in the surface-applied plots were similar to, whereas subsurface injection profiles were different from, that of the unamended soils. Forty-six days after manure application, the soil ARG profiles in manure injection slits were 37% more diverse than that of the unamended plots. The abundance of manure-associated ARGs were lower in surface runoff from manure subsurface injected plots and carried a lower resistome risk score in comparison to surface-applied plots. This study demonstrated, for the first time, that although manure subsurface injection reduces ARGs in the runoff, it can create potential long-term hotspots for elevated ARGs within injection slits.

[Breast milk microbiota of mothers with different glucose tolerance at 42 days postpartum].

OBJECTIVE: To compare the differences in microbial community between lactating mothers with gestational diabetes mellitus(GDM) and normal glucose tolerance lactating mothers(control) at 42 days postpartum, and to explore the effect of GDM on the microbial composition and structure of breast milk. METHODS: A total of 21 mothers with GDM and 25 healthy mothers in Fuqing Maternity and Child Health Care Hospital at 42 days postpartum from May 2019 to September 2020 were enrolled. A questionnaire was used to collect the basic information and dietary intakes of mothers. The mother's milk was collected by using a sterile electric breast pump. Breast milk microbiota profiles were assessed by 16 S rDNA gene amplicon based sequencing of the V3-V4 region and the sequencing platform was Illumina Miseq PE3000, bioinformatics analysis was performed on the sequencing result. RESULTS: Compared with the control group, the mothers in the GDM group consumed more vegetables(222.7(190.6, 333.1)g/d vs.176.4(49.5, 247.0)g/d, P=0.042). There was no significant difference in Alpha diversity between the two groups(P>0.05). Beta diversity analysis showed that there were significant differences in the microbial composition between the two groups(P<0.01). Breast milk microbiota species difference analysis showed that there were differences in several species between GDM group and NGT group at the levels from phylum to genus. Compared with control group, the relative abundance of Bacteroidota and Cyanobacteria in GDM group decreased significantly [(3.41±2.59)% vs. (1.23±0.82)%, (1.08±3.02)% vs. (0.10±0.11)%, P<0.05]. In the GDM group, Ralstonia, Rhodococcus, Burkholderia-Caballeronia-Paraburkholderia, Acinetobacter and Fluviicola were decreased((38.93±28.85)% vs. (26.70±28.37)%, (9.23±6.87)% vs. (4.88±6.03)%, (7.66±4.80)% vs. (2.77±1.33)%, (6.18±11.90)% vs. (2.76±6.10)%, (1.21±1.31)% vs. (0.33±0.62)%, P<0.05). The unclassified＿f＿＿xanthobacteraceae was increased, and the difference was statistically significant((0.85±3.15)% vs. (23.64±23.63)%, P<0.05). CONCLUSION: There are differences in breast milk microbial community structure in women with different glucose tolerance at 42 days postpartum, Ralstonia, Rhodococcus, Burkholderia-Caballeronia-Paraburkholderia, Acinetobacter and Fluviicola were significantly lower comparing to the normal glucose tolerance mothers.

Monitoring of spatiotemporal occupancy patterns of fish and amphibian species in a lentic aquatic system using environmental DNA.

To effectively monitor, manage and protect aquatic species and understand their interactions, knowledge of their spatiotemporal distribution is needed. In this study, we used a fine-scale spatiotemporal water sampling design, followed by environmental DNA (eDNA) 12S metabarcoding, to investigate occupancy patterns of a natural community of fish and amphibian species in a lentic system. In the same system, we experimentally estimated the spatial and temporal dispersion of eDNA by placing a community of different fish and amphibian species in cages at one side of the pond, creating a controlled point of eDNA emission. Analyses of this cage community revealed a sharp spatial decline in detection rates and relative eDNA quantities at a distance of 5-10 m from the source, depending on the species and its abundance. In addition, none of the caged species could be detected 1 week after removal from the system. This indicates high eDNA decay rates and limited spatial eDNA dispersal, facilitating high local resolution for monitoring spatial occupancy patterns of aquatic species. Remarkably, for seven of the nine cage species, the presence of a single individual could be detected by pooling water of subsamples taken across the whole water body, illustrating the high sensitivity of the eDNA sampling and detection method applied. Finally, our work demonstrated that a fine-scale sampling design in combination with eDNA metabarcoding can cover total biodiversity very precisely and allows the construction of consistent spatiotemporal patterns of relative abundance and local distribution of free-living fish and amphibian species in a lentic ecosystem.

Implications of 2D versus 3D surveys to measure the abundance and composition of benthic coral reef communities.

A paramount challenge in coral reef ecology is to estimate the abundance and composition of the communities residing in such complex ecosystems. Traditional 2D projected surface cover estimates neglect the 3D structure of reefs and reef organisms, overlook communities residing in cryptic reef habitats (e.g., overhangs, cavities), and thus may fail to represent biomass estimates needed to assess trophic ecology and reef function. Here, we surveyed the 3D surface cover, biovolume, and biomass (i.e., ash-free dry weight) of all major benthic taxa on 12 coral reef stations on the island of Curaçao (Southern Caribbean) using structure-from-motion photogrammetry, coral point counts, in situ measurements, and elemental analysis. We then compared our 3D benthic community estimates to corresponding estimates of traditional 2D projected surface cover to explore the differences in benthic community composition using different metrics. Overall, 2D cover was dominated (52 ± 2%, mean ± SE) by non-calcifying phototrophs (macroalgae, turf algae, benthic cyanobacterial mats), but their contribution to total reef biomass was minor (3.2 ± 0.6%). In contrast, coral cover (32 ± 2%) more closely resembled coral biomass (27 ± 6%). The relative contribution of erect organisms, such as gorgonians and massive sponges, to 2D cover was twofold and 11-fold lower, respectively, than their contribution to reef biomass. Cryptic surface area (3.3 ± 0.2 m2 m-2 planar reef) comprised half of the total reef substrate, rendering two thirds of coralline algae and almost all encrusting sponges (99.8%) undetected in traditional assessments. Yet, encrusting sponges dominated reef biomass (35 ± 18%). Based on our quantification of exposed and cryptic reef communities using different metrics, we suggest adjustments to current monitoring approaches and highlight ramifications for evaluating the ecological contributions of different taxa to overall reef function. To this end, our metric conversions can complement other benthic assessments to generate non-invasive estimates of the biovolume, biomass, and elemental composition (i.e., standing stocks of organic carbon and nitrogen) of Caribbean coral reef communities. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00338-021-02118-6.

Timepoint Selection Strategy for In Vivo Proteome Dynamics from Heavy Water Metabolic Labeling and LC-MS.

Protein homeostasis, proteostasis, is essential for healthy cell functioning and is dysregulated in many diseases. Metabolic labeling with heavy water followed by liquid chromatography coupled online to mass spectrometry (LC-MS) is a powerful high-throughput technique to study proteome dynamics in vivo. Longer labeling duration and dense timepoint sampling (TPS) of tissues provide accurate proteome dynamics estimations. However, the experiments are expensive, and they require animal housing and care, as well as labeling with stable isotopes. Often, the animals are sacrificed at selected timepoints to collect tissues. Therefore, it is necessary to optimize TPS for a given number of sampling points and labeling duration and target a specific tissue of study. Currently, such techniques are missing in proteomics. Here, we report on a formula-based stochastic simulation strategy for TPS for in vivo studies with heavy water metabolic labeling and LC-MS. We model the rate constant (lognormal), measurement error (Laplace), peptide length (gamma), relative abundance of the monoisotopic peak (beta regression), and the number of exchangeable hydrogens (gamma regression). The parameters of the distributions are determined using the corresponding empirical probability density functions from a large-scale dataset of murine heart proteome. The models are used in the simulations of the rate constant to minimize the root-mean-square error (rmse). The rmse for different TPSs shows structured patterns. They are analyzed to elucidate common features in the patterns.

Conspecific distance-dependent seedling performance, and replacement of conspecific seedlings by heterospecifics in five hardwood, temperate forest species.

The mechanisms driving species diversity in the context of Janzen-Connell model are best understood by evaluating not only conspecific distance-dependent (CDD) seedling performance, but also replacement of conspecific seedlings by heterospecific seedlings beneath adult trees. We evaluated CDD and replacement as a log response ratio of seedling performance (height, age) directly beneath and at a distance from adult plants in a temperate forest, and examined the log response ratio of that between conspecifics and heterospecifics beneath adults for five hardwood species with different ecological traits (e.g., seed size, mycorrhizal type, relative abundance). CDD was greater in three small-seeded species with arbuscular mycorrhizae (AM) associations than it was in two large-seeded species with ectomycorrhizae (EM) associations. Replacement was also higher for small-seeded AM species compared to large-seeded EM species, resulting in a strong, positive relationship between CDD and replacement. The traits suggest that small-seeded AM seedlings are more likely to be replaced by heterologous seedlings beneath the adults than large-seeded EM seedlings, probably due to that the small-seeded AM species are more susceptible to attack by plant natural enemies (e.g., soil pathogens, leaf diseases). As a result, small-seeded AM species had lower relative abundances compared to large-seeded EM species. This study suggests that either seed size or associations with microorganisms play an important role in driving forest diversity by regulating replacement and CDD, although relative importance of the two traits (i.e., seed size, mycorrhizal type) remains unclear, because of the autocorrelation between the two traits for the five species studied.

Identification of the metabolites of isochlorogenic acid A in rats by UHPLC-Q-Exactive Orbitrap MS.

CONTENT: Isochlorogenic acid A, one of the main components of Duhaldea nervosa (Wallich ex Candolle) A. Anderberg (Asteraceae), is a folk medicine used to treat a variety of diseases including fracture and rheumatoid arthritis. Despite its widespread use, the metabolism of isochlorogenic acid A in vivo has not been fully studied. OBJECTIVE: An analytical strategy based on UHPLC-Q-Exactive Orbitrap MS is proposed for the detection and identification of the metabolites of isochlorogenic acid A in rats. MATERIALS AND METHODS: Six male Sprague-Dawley rats (180 ± 20 g) were randomly divided into two groups. Then, blood and tissue samples were obtained after oral administration of isochlorogenic acid A (200 mg/kg). All the samples were pre-treated by the Solid Phase Extraction (SPE) method. Next, the samples were analysed by UHPLC-Q-Exactive Orbitrap MS. Finally, the metabolites were identified based on the metabolomic workflow template. RESULTS: A total of 33 metabolites were identified in rat plasma, with 30 of them being reported for the first time. The distribution of all metabolites in tissues was first investigated, three of them were widely distributed in liver, lungs, and kidneys. The corresponding reactions including methylation, hydrolysis, sulphate conjugation, glucuronide conjugation, as well as their composite reactions, are reported in this study. DISCUSSION AND CONCLUSIONS: This method has wide-scale application prospects in the identification of metabolites. Considering that limited research has been conducted in this area, this study proposes metabolic pathways to further understand mechanisms of isochlorogenic acid A and the forms that are truly effective in vivo.

metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models.

BACKGROUND: The rapid growth of high-throughput sequencing-based microbiome profiling has yielded tremendous insights into human health and physiology. Data generated from high-throughput sequencing of 16S rRNA gene amplicons are often preprocessed into composition or relative abundance. However, reproducibility has been lacking due to the myriad of different experimental and computational approaches taken in these studies. Microbiome studies may report varying results on the same topic, therefore, meta-analyses examining different microbiome studies to provide consistent and robust results are important. So far, there is still a lack of implemented methods to properly examine differential relative abundances of microbial taxonomies and to perform meta-analysis examining the heterogeneity and overall effects across microbiome studies. RESULTS: We developed an R package 'metamicrobiomeR' that applies Generalized Additive Models for Location, Scale and Shape (GAMLSS) with a zero-inflated beta (BEZI) family (GAMLSS-BEZI) for analysis of microbiome relative abundance datasets. Both simulation studies and application to real microbiome data demonstrate that GAMLSS-BEZI well performs in testing differential relative abundances of microbial taxonomies. Importantly, the estimates from GAMLSS-BEZI are log (odds ratio) of relative abundances between comparison groups and thus are analogous between microbiome studies. As such, we also apply random effects meta-analysis models to pool estimates and their standard errors across microbiome studies. We demonstrate the meta-analysis examples and highlight the utility of our package on four studies comparing gut microbiomes between male and female infants in the first six months of life. CONCLUSIONS: GAMLSS-BEZI allows proper examination of microbiome relative abundance data. Random effects meta-analysis models can be directly applied to pool comparable estimates and their standard errors to evaluate the overall effects and heterogeneity across microbiome studies. The examples and workflow using our 'metamicrobiomeR' package are reproducible and applicable for the analyses and meta-analyses of other microbiome studies.