Changes In Microbial Diversity Research Articles

Drainage gradient versus seasonal cycles: Differential response of microbial community composition to variations in soil moisture

AbstractThe variation in the soil microbial community composition over time was assessed at monthly time steps for 1 year in three neighboring Mollisols spanning a drainage gradient. This was done to distinguish between natural oscillations in the community composition versus lasting adaptations to environmental factors such as soil water availability. To isolate soil water availability as a controlling factor, we selected three soils sharing the same soil order (fine‐silty, superactive Argixerolls/Argialbolls); slope (0%–1%); temperature regime (mesic); moisture regime (xeric); and land use history (continuous grassland for the past 10 years) but differing in drainage class (well‐drained vs. moderately well‐drained vs. poorly drained). Changes in microbial diversity were quantified by monitoring the bacterial community at monthly intervals for 1 year. Within individual soils, α‐diversity varied little with season and drainage classes. Despite the three soils experiencing the same climate regime and vegetation/land use, they exhibited distinct community composition and turnover, which we attribute to differences in moisture availability across drainage and seasons. We posit that a seasonal recurring drop in soil redox potential induced by seasonal water saturation in the poorly drained soil is the most probable cause setting the microbial community of that soil apart from those in the better drained soils. Our investigation suggests that not all indicators of microbial diversity share the same sensitivity to seasonal and drainage‐related soil moisture variations.

Impact of Agroforestry Practices on Soil Microbial Diversity and Nutrient Cycling in Atlantic Rainforest Cocoa Systems

Microorganisms are critical indicators of soil quality due to their essential role in maintaining ecosystem services. However, anthropogenic activities can disrupt the vital metabolic functions of these microorganisms. Considering that soil biology is often underestimated and traditional assessment methods do not capture its complexity, molecular methods can be used to assess soil health more effectively. This study aimed to identify the changes in soil microbial diversity and activity under different cocoa agroforestry systems, specially focusing on taxa and functions associated to carbon and nitrogen cycling. Soils from three different cocoa agroforestry systems, including a newly established agroforestry with green fertilization (GF), rubber (Hevea brasiliensis)–cocoa intercropping (RC), and cocoa plantations under Cabruca (cultivated under the shave of native forest) (CAB) were analyzed and compared using metagenomic and metaproteomic approaches. Samples from surrounding native forest and pasture were used in the comparison, representing natural and anthropomorphic ecosystems. Metagenomic analysis revealed a significant increase in Proteobacteria and Basidiomycota and the genes associated with dissimilatory nitrate reduction in the RC and CAB areas. The green fertilization area showed increased nitrogen cycling activity, demonstrating the success of the practice. In addition, metaproteomic analyses detected enzymes such as dehydrogenases in RC and native forest soils, indicating higher metabolic activity in these soils. These findings underscore the importance of soil management strategies to enhance soil productivity, diversity, and overall soil health. Molecular tools are useful to demonstrate how changes in agricultural practices directly influence the microbial community, affecting soil health.

Evaluating the Effects of Non-Nutritive Sweeteners on Pigs: A Systematic Review.

Non-nutritive sweeteners (NNS) have been investigated for their potential to improve feed palatability and growth performance in pigs, although their use in swine production remains limited. This systematic review evaluates the effects of NNS on pigs, drawing from 18 studies published between 1990 and 2024. Following the PRISMA guidelines and using the PICOS framework, a total of 448 papers were initially identified, of which 18 met the inclusion criteria for review. The results are mixed: some studies suggest that NNS like stevioside, sucralose, and neotame may improve performance and reduce diarrhea, while others show limited or no effects. The impact of NNS on gut microbiota is similarly inconsistent, with some sweeteners promoting beneficial bacterial growth, while others show minimal changes in microbial diversity. This review emphasizes the need for more research to clarify the effects of NNS in pigs, particularly the mechanisms behind their influence on growth and gut health. Additionally, further studies are needed to determine optimal dosages and assess the long-term impacts of NNS on pig immune function and overall health. The findings highlight the current gaps in knowledge and suggest that more evidence is needed to understand the role of NNS in swine nutrition.

Faba bean-wheat intercropping controls the occurrence of faba bean Fusarium wilt by improving the microecological environment of rhizosphere soil

BackgroundFusarium wilt is a severe soil-borne disease that affects faba bean production. Faba bean-wheat intercropping is often used to control the occurrence of Fusarium wilt in faba bean. AimsTo evaluate the effects of faba bean-wheat intercropping on the occurrence of faba bean Fusarium wilt and soil microecology. MethodsWe established two planting patterns, faba bean monocropping (M) and faba bean-wheat intercropping (I), to investigate Fusarium wilt occurrence and plant dry weight and assess changes in soil enzyme activities, microbial diversity, and community composition during different stages of disease onset. ResultsIntercropping effectively controlled faba bean Fusarium wilt at the three disease stages and increased the dry weight of faba bean plants. Intercropping promoted the activities of catalase (CAT), urease, sucrase, and acid phosphatase in the rhizosphere soil of faba bean at three disease stages. Bacterial and fungal diversity decreased with disease progression, and intercropping mitigated this trend. Compared with monocropping, intercropping increased the abundance of beneficial bacteria such as Proteobacteria, Actinobacteriota, Gemmatimonadota, Gemmatimonas, Conexibacter, and Sphingomonas, while reducing the abundance of pathogenic fungi such as Alternaria, Cladosporium, and Fusarium. Intercropping also increased the abundance of arbuscular mycorrhiza, soil saprophytes, and undefined saprophytes while decreasing the abundance of plant pathogens. ConclusionFaba bean-wheat intercropping enhanced soil enzyme activities, effective nutrient content, and alpha diversity indices of bacteria and fungi in the rhizosphere soil of faba bean, while promoting the abundance of beneficial bacteria, arbuscular mycorrhizal fungi, as well as both soil and undefined humus. Simultaneously, intercropping reduced the abundance of plant pathogens, facilitated nutrient cycling in the soil, provided sufficient nutrients for crop uptake, and mitigated the toxic effects of hydrogen peroxide on cells. Ultimately, this resulted in a reduced occurrence of Fusarium wilt.

Gut Microbiota Alterations in Alzheimer's Disease: Relation with Cognitive Impairment and Mediterranean Lifestyle.

Recently, an association between dysbiosis of the gut microbiota (GMB) and the development of several diseases, such as Alzheimer's disease (AD), has been proposed. Dysbiosis involves changes in microbial diversity influenced by environmental factors, like diet or lifestyle. In this study, we investigated the role of GMB parameters in Spanish AD patients, assessing the impact of adherence to the Mediterranean lifestyle (ML), as well as to characterize these parameters in relation to neuropsychological, neuropsychiatric, emotional, and functionality parameters. A case-control study was conducted to investigate the association between the composition of the GMB and cognitive, emotional, neuropsychiatric, and functionality status in Spanish AD patients, along with a shotgun metagenomics approach. Richness and alpha-diversity were significantly lower in the AD group compared to the controls. PERMANOVA and ANOSIM tests of Bray-Curtis dissimilarity, Aitchison distance, and Jaccard similarity did not showed significant differences in beta-diversity between the two groups. Moreover, associations between various phyla of the AD group and orientation performance, food consumption, and activities of daily living were identified. Dysbiosis observed in Spanish AD patients is characterized by reductions in richness and alpha-diversity, alongside alterations in GMB composition, which may be linked to adherence to the ML and cognitive and functionality symptoms.

The effects of high-precision scale dispersant concentrations on microbial community and new implications for dispersant application after marine oil spills

The usage of dispersant presents a difficult choice: the uncertainty of beneficial biodegradation of spilled oil against what could be a greater environmental impact from the finely dispersed oil. Here, we evaluated the effect of dispersant on the microbial community at a high-precision concentration (0.1–20 % (v/v), 10 gradients) to elucidate the uncertainty of beneficial biodegradation and proposed the associated mechanism. Results at the phylum, class, and genus level revealed no significant changes in microbial diversity and structure at low-concentration dispersants (0.1–3 %), but significant changes at high-concentration dispersants (5–20 %). For beneficial biodegradation, 4 oil-degrading bacteria and 3 non-oil-degrading bacteria exhibited strong positive (R2 > 0.72) and negative (R2 > 0.73) correlations at 0.1–3 % low-concentrations. More importantly, oil-degrading bacteria abundance exceeded 75.9 % in the total abundance proportion (70.1 %) of them. This indicated low-concentration dispersants can promote biodegradation. In the high-concentrations, similar but opposite results were shown. Therefore, dispersant concentration dominates biodegradation of spilled oil. Finally, we proposed the associated “bacterial peaking” mechanism and clarified that biodegradation increases under the drive of the affected bacteria and reach a peak at low-concentration dispersants, but decline rapidly at high-concentrations. This study provided a new insight to understand the usage of dispersant on biodegradation of spilled oil in the sea.

Leguminous green mulching alters the microbial community structure and increases microbial diversity by improving nitrogen availability in subtropical orchard systems in China

Microorganisms, the major decomposers of plant residues, are crucial for soil nutrient cycling. Living grass mulching effectively alters microbial community structure and promotes nutrient cycling. However, its consistency with mulching ages and growth periods remains unclear. Therefore, this study aims to clarify the dynamic characteristics of microbial communities and enzyme activities across different mulching ages. In this study, high-throughput sequencing technology was used to investigate bacterial and fungal community evolution in three mulching treatments with Vicia villosa for 8 years (VV_8), 4 years (VV_4), and clean tillage in a citrus orchard. This study covered three growth periods (citrus–grass: spring sprouting to budding period [SSBP], fruit swelling to withering period [FSWP], and fruit maturity to seeding period [FMSP]). The results showed that VV_4 and VV_8 treatments increased bacterial and fungal alpha diversity as well as the activities of nitrogen (N), carbon (C), and phosphorus cycling enzymes. C-cycling enzyme activity was the primary key factor driving changes in microbial diversity across growth periods. Under leguminous green mulching, bacteria alpha diversity increased the most during FSWP, while fungi increased the most during FMSP. Additionally, the relative abundance of Ascomycota and Basidiomycota significantly increased during the FSWP and FMSP, reaching 63.65–73.80 % and 79.73–84.51 %, respectively. With increasing mulching ages, the structural stability and synergistic effects of microorganisms were correspondingly enhanced. Furthermore, available nutrients determined microbial community evolution, with N availability being a key factor influencing microbial diversity, especially fungal diversity. In conclusion, as mulching ages increase, improved nutrient availability gradually enhances microbial diversity, synergistic interactions, and nutrient cycling functions, with copiotrophic taxa occupying a key position in the microbial network. FSWP is a critical turning point for enhancing microbial activity and C-cycling function. This study offers theoretical support for developing microbial regulation strategies to improve soil quality in orchard management practices.

Effects of High Amylose-Resistant Starch on Gut Microbiota and Uremic Toxin Levels in Patients With Stage-G3a-G4 Chronic Kidney Disease: A Randomized Trial

ObjectiveThis study was designed to determine the effect of 16 weeks of supplementation with Hi-maize 260 resistant starch on the gut microbiota, uremic toxins (indoxyl sulfate and p-cresyl sulfate), markers of inflammation and oxidative stress along with vascular function in patients with stage G3a-G4 chronic kidney disease (CKD). Design& Methods: This was a double-blind, placebo-controlled, parallel-arm, randomized controlled trial. Sixty-eight patients with stage G3a-G4 CKD were randomized to either resistant starch with usual care or placebo and usual care. Patients attended four testing sessions: two baseline visits, and follow-up visits at 8 and 16 weeks. Fasting blood samples, resting brachial and central blood pressures, along with arterial stiffness, were collected at visits (1 or 2), and weeks 8 and 16. A stool sample was collected for analysis of microbial composition at baseline and week 16. Patients were randomized after the baseline visits. ResultsPatients receiving the resistant starch had a reduction in p-cresyl sulfate at week 16. This reduction was associated with a decrease in microbial α-diversity between baseline and week 16 (Chao1 p=0.014, Shannon p=0.017, PD p= 0.046, and Simpson p=0.017) as well as increases in Subdoligranulum (p=0.03) and Oscillospiraceae UCG 002 (p=0.02) and decreases in Bacteroides (p=0.009).There were no changes in microbial beta diversity and other biomarkers or markers of vascular function following the 16-week period Conclusion: Sixteen weeks of supplementation of resistant starch in patients with stage G3a-G4 CKD led to changes in microbial composition that were associated with a significant reduction in p-cresyl sulfate.

Influence of Peanut Consumption on the Gut Microbiome: A Randomized Clinical Trial.

Background: Peanut consumption could impact cardiometabolic health through gut microbiota, a hypothesis that remains to be investigated. A randomized clinical trial in Vietnam evaluated whether peanut consumption alters gut microbiome communities. Methods: One hundred individuals were included and randomly assigned to the peanut intervention and control groups. A total of 51 participants were provided with and asked to consume 50 g of peanuts daily, while 49 controls maintained their usual dietary intake for 16 weeks. Stool samples were collected before and on the last day of the trial. After excluding 22 non-compliant participants and those who received antibiotic treatment, 35 participants from the intervention and 43 from the control were included in the analysis. Gut microbiota composition was measured by shotgun metagenomic sequencing. Associations of changes in gut microbial diversity with peanut intervention were evaluated via linear regression analysis. Linear mixed-effects models were used to analyze associations of composition, sub-community structure, and microbial metabolic pathways with peanut intervention. We also performed beta regression analysis to examine the impact of peanut intervention on the overall and individual stability of microbial taxa and metabolic pathways. All associations with false discovery rate (FDR)-corrected p-values of <0.1 were considered statistically significant. Results: No significant changes were found in α- and β-diversities and overall gut microbial stability after peanut intervention. However, the peanut intervention led to lower enrichment of five phyla, five classes, two orders, twenty-four metabolic pathways, and six species-level sub-communities, with a dominant representation of Bifidobacterium pseudocatenulatum, Escherichia coli D, Holdemanella biformis, Ruminococcus D bicirculans, Roseburia inulinivorans, and MGYG-HGUT-00200 (p < 0.05 and FDR < 0.1). The peanut intervention led to the short-term stability of several species, such as Faecalibacterium prausnitzii F and H, and a metabolic pathway involved in nitrate reduction V (p < 0.05; FDR < 0.1), known for their potential roles in human health, especially cardiovascular health. Conclusions: In summary, a 16-week peanut intervention led to significant changes in gut microbial composition, species-level sub-communities, and the short-term stability of several bacteria, but not overall gut microbial diversity and stability. Further research with a larger sample size and a longer intervention period is needed to confirm these findings and investigate the direct impact of gut-microbiome-mediated health effects of peanut consumption. Trial registration: The International Traditional Medicine Clinical Trial Registry (ITMCTR). Registration number: ITMCTR2024000050. Retrospectively Registered 24 April 2024.

Garlic-Induced Enhancement of Bifidobacterium: Enterotype-Specific Modulation of Gut Microbiota and Probiotic Populations

The gut microbiome is a dynamic ecosystem crucial for maintaining its host’s health by regulating various immune and metabolic functions. Since diet plays a fundamental role in shaping the gut microbiome, understanding the relationship between food consumption and microbiome structure is essential. Although medicinal plants are widely recognized for their broad health benefits, their specific impact on the gut microbiome remains unclear. In this study, we investigated the effects of garlic (Allium sativum) on the gut microbiome using an in vitro human fecal incubation model. Our findings revealed that the impact of garlic on gut microbial structure varied depending on the dominant gut microbiome components (enterotypes). The Bacteroides-dominant enterotype exhibited significant changes in overall microbial diversity in response to garlic, while the Prevotella-dominant enterotype remained unaffected. Additionally, the garlic treatment led to specific alterations in microbiota composition, such as an increase in beneficial probiotics like Bifidobacterium. We validated garlic’s prebiotic potential by promoting the growth of Bifidobacterium adolescentis under in vitro culture conditions. Our study highlights the importance of understanding enterotype-specific responses to diet and suggests that garlic may serve as a dietary supplement for modulating gut microbiota and promoting the growth of beneficial probiotics.

Depuration of Asian Green Mussels Using Chitooligosaccharide-Epigallocatechin Gallate Conjugate: Shelf-Life Extension, Microbial Diversity, and Quality Changes during Refrigerated Storage

The effect of chitooligosaccharide-EGCG conjugate (CEC) at different concentrations (0, 1, and 2%; w/v) and depuration times (DT; 3, and 6 h) on the total viable count and Vibrio spp. count of Asian green mussels (AGMs) was studied. Depurated samples showed a reduction in both microbial counts as compared to fresh AGMs (without depuration) and AGMs depurated using water (CON). A similar TVC was noticed at both DTs; however, a lower VC was attained at a DT of 3, irrespective of CEC concentrations (p &lt; 0.05). AGMs were depurated for 3 h using 1 and 2% CEC (CE1 and CE2, respectively) solutions and stored for 6 days at 4 °C. The CE2 sample showed the lowest microbial counts as compared to fresh AGMs, CON, and CE1 throughout the storage (p &lt; 0.05). CE2 extended the shelf-life of AGMs by 4 days, which was also supported by the lower peroxide value (0.48 mg cumene hydroperoxide/kg sample) and TBARS (0.94 mmol MDA eqv/kg sample) when compared with other samples. Moreover, CE2 had a lower total volatile nitrogen base (TVB; 4.72 mg N/100 g) and trimethylamine (TMA; 3.59 mg N/100 g) on day 4. Furthermore, 2% CEC was able to maintain the DHA content; however, a slightly lower EPA was noticed as compared to the CON. Next-generation sequencing suggested that the CON had a larger microbial community, especially Vibrio sp., than the CE2. All the treated samples showed similar likeness scores to the cooked CE2 and CON on day 0. However, slightly lower likeness was attained when CE2 was stored for 4 days, but the likeness score was higher than the acceptable limit (5). No difference in cooking loss was noticed between CON and CE2 samples on day 0. Nevertheless, cooking loss was increased on day 4. Thus, depuration using CEC solution enhanced the shelf-life of AGMs by 4 days without having negative impact on consumer acceptability and textural properties.

Taxonomic variation, plastic degradation, and antibiotic resistance traits of plastisphere communities in the maturation pond of a wastewater treatment plant.

Wastewater treatment facilities can filter out some plastics before they reach the open environment, yet microplastics often persist throughout these systems. As they age, microplastics in wastewater may both leach and sorb pollutants and fragment to provide an increased surface area for bacterial attachment and conjugation, possibly impacting antimicrobial resistance (AMR) traits. Despite this, little is known about the effects of persistent plastic pollution on microbial functioning. To address this knowledge gap, we deployed five different artificially weathered plastic types and a glass control into the final maturation pond of a municipal wastewater treatment plant in Ōtautahi-Christchurch, Aotearoa/New Zealand. We sampled the plastic-associated biofilms (plastisphere) at 2, 6, 26, and 52 weeks, along with the ambient pond water, at three different depths (20, 40, and 60 cm from the pond water surface). We investigated the changes in plastisphere microbial diversity and functional potential through metagenomic sequencing. Bacterial 16S ribosomal RNA genes composition did not vary among plastic types and glass controls (P = 0.997) but varied among sampling times [permutational multivariate analysis of variance (PERMANOVA), P = 0.001] and depths (PERMANOVA, P = 0.011). Overall, there was no polymer-substrate specificity evident in the total composition of genes (PERMANOVA, P = 0.67), but sampling time (PERMANOVA, P = 0.002) and depth were significant factors (PERMANOVA, P = 0.001). The plastisphere housed diverse AMR gene families, potentially influenced by biofilm-meditated conjugation. The plastisphere also harbored an increased abundance of genes associated with the biodegradation of nylon, or nylon-associated substances, including nylon oligomer-degrading enzymes and hydrolases.IMPORTANCEPlastic pollution is pervasive and ubiquitous. Occurrences of plastics causing entanglement or ingestion, the leaching of toxic additives and persistent organic pollutants from environmental plastics, and their consequences for marine macrofauna are widely reported. However, little is known about the effects of persistent plastic pollution on microbial functioning. Shotgun metagenomics sequencing provides us with the necessary tools to examine broad-scale community functioning to further investigate how plastics influence microbial communities. This study provides insight into the functional consequence of continued exposure to waste plastic by comparing the prokaryotic functional potential of biofilms on five types of plastic [linear low-density polyethylene (LLDPE), nylon-6, polyethylene terephthalate, polylactic acid, and oxygen-degradable LLDPE], glass, and ambient pond water over 12 months and at different depths (20, 40, and 60 cm) within a tertiary maturation pond of a municipal wastewater treatment plant.

Gut microbiota dynamics of adult and sub‐adult sika deer during reintroduction

AbstractPrey populations significantly influence the distribution of top predators. The sika deer (Cervus nippon), a key prey species for the Amur tiger in Northeast China, plays a critical role in the recovery and dispersal of Amur tiger populations. Reintroduction is a pivotal strategy for restoring prey populations, but it presents challenges, especially in terms of adaptation to the natural environment during the natural training process before animals are released. In this study, we sampled six adult and six sub‐adult sika deer and employed high‐throughput sequencing of the 16S ribosomal RNA gene to investigate changes in gut microbial diversity, composition, and function during natural training. The results showed that adult sika deer had higher gut microbiota diversity compared to sub‐adults. However, as natural training progressed, the gut microbial diversity in sub‐adults approached that of adults. Additionally, beneficial, fiber‐digesting bacteria associated with adaptation to the natural environment tended to increase during nature training in both adult and sub‐adult sika deer, while pathogenic bacteria tended to decrease. We also compared the metabolic function of the gut microbiota in adult and sub‐adult sika deer, which showed that the carbohydrate metabolic function of both adults and sub‐adults decreased significantly with natural training, declining more rapidly in sub‐adults. Conversely, the lipid metabolic function in sub‐adults increased significantly with natural training. Overall, a period of nature training is necessary before reintroducing animals to their natural habitats, and sub‐adult sika deer, in particular, exhibit greater adaptability to environmental changes as reflected by their gut microbiota dynamics. These findings offer valuable insights for the reintroduction of sika deer and other ungulates. We recommend incorporating natural training in reintroduction programs and prioritizing sub‐adult animals for reintroduction.

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.

PSVII-25 Contributions to bacterial diversity of the piglet pioneer microbiome

Abstract The establishment of the gastrointestinal tract microbiome of the neonate, or pioneer microbiome, can predetermine the health and performance of the newborn. Previous work has established that both maternal and environmental sources are capable of shifting the pioneer microbial composition. Despite this, proportional quantifications of the maternal and environmental factors that influence the bacterial diversity of the piglet pioneer microbiome have yet to be evaluated. Therefore, the objective of this study was to determine the contributions from both maternal and environmental origins on piglet pioneer bacterial diversity. Sterile swab samples were collected from farrowing crates prior to (EMPTYCRATE) and after gilts were housed (FULLCRATE; n = 5; Landrace x Yorkshire x Duroc), gilt vaginas at farrowing (BIRTHCANAL), and piglet rectums on d 0 (pre-suckling), 3, and 10 post-farrowing and at weaning (21.6 ± 1.0 d post-farrowing). Colostrum (COLOSTRUM) from a representative number of teats was also collected from each gilt at farrowing into sterile collection cups. All samples were stored at -80°C until subsequent analyses. Gene sequencing for microbiome analysis targeted the V4 hypervariable region of the 16S rRNA bacterial gene. Sequence quality was assessed utilizing DADA2, and taxon analysis and diversity metrics were processed in the qiime2 pipeline. Alpha diversity (within sample) metrics were analyzed with Kruskal-Wallis, and beta diversity (between sample) metrics were assessed with PERMANOVA. Alpha diversity analyses included Pielou’s evenness index (i.e., within sample distribution), Shannon’s diversity index (i.e., within sample richness and evenness), observed OTUs (i.e., within sample richness), and Faith’s diversity index (i.e. within sample richness and phylogeny). Pielou’s evenness index (P = 0.027) and Shannon’s diversity index (P = 0.086) indicated differences between EMPTYCRATE and FULLCRATE. However, no differences were detected between the environmental sources for observed OTUs or Faith’s diversity index. Piglet samples by day were different for observed OTUs (P = 0.002), Faith’s diversity index (P = 0.0002), and Shannon’s diversity index (P = 0.073), which all consider bacterial richness within the samples. Specifically, the piglet d 3 samples were the least for these three metrics; however, there were no differences in Pielou’s evenness index for all piglet by day samples. There were no differences for all alpha diversity metrics between BIRTHCANAL and COLOSTRUM. Beta diversity metrics included unweighted UniFrac (i.e., between sample bacterial presence or absence) and weighted UniFrac (i.e., between sample bacterial presence or absence and abundance). Evaluation between the maternal contributions BIRTHCANAL and COLOSTRUM indicated differences for both unweighted UniFrac (P = 0.011) and weighted UniFrac (P = 0.007). Bacterial diversity between the environmental origins EMPTYCRATE and FULLCRATE were also different for unweighted UniFrac (P = 0.012) and weighted UniFrac (P = 0.038). There were no differences in beta diversity between all piglet by day samples. These results indicate that both maternal and environmental sources contribute to changes in piglet pioneer microbial diversity during early neonatal life.

Inflammation mediated by gut microbiome alterations promotes lung cancer development and an immunosuppressed tumor microenvironment.

Accumulating evidence indicates that the gut microbiome influences cancer progression and therapy. We recently showed that progressive changes in gut microbial diversity and composition are closely associated with tobacco-associated lung adenocarcinoma (LUAD) in a human-relevant mouse model. Furthermore, we demonstrated that the loss of the antimicrobial protein Lcn2 in these mice, exacerbates pro-tumor inflammatory phenotypes while further reducing microbial diversity. Yet, how gut microbiome alterations impinge on LUAD development remains poorly understood. Here, we investigated the role of gut microbiome changes in LUAD development using fecal microbiota transfer and delineated a pathway by which gut microbiome alterations incurred by loss of Lcn2 fostered the proliferation of pro-inflammatory bacteria of the genus Alistipes, triggering gut inflammation. This inflammation propagated systemically, exerting immunosuppression within the tumor microenvironment, augmenting tumor growth through an IL-6-dependent mechanism and dampening response to immunotherapy. Corroborating our preclinical findings, we found that patients with LUAD with a higher relative abundance of Alistipes species in the gut showed diminished response to neoadjuvant immunotherapy. These insights reveal the role of microbiome-induced inflammation in LUAD and present new potential targets for interception and therapy.

Assembly process and co-occurrence network of microbial community in response to free ammonia gradient distribution.

The research presented in this paper explores how varying concentrations of free ammonia impact microbial communities in aquatic ecosystems. By employing advanced gene sequencing techniques, the study reveals significant changes in microbial diversity and network structures in response to increased ammonia levels. Key findings indicate that high ammonia concentrations lead to a decrease in microbial richness and diversity while increasing community dissimilarity. Notably, certain microbial groups, like Actinobacteria, show resilience to ammonia stress. This research enhances our understanding of how pollution affects microbial ecosystems and underscores the importance of maintaining balanced ammonia levels to preserve microbial diversity and ecosystem health.

Morphological and Microbial Diversity of Hydromagnesite Microbialites in Lake Salda: A Mars Analog Alkaline Lake

ABSTRACTLake Salda, a terrestrial analog for the paleolake in Jezero Crater on Mars, hosts active, subfossil, and fossil hydromagnesite microbialites, making it an ideal location to study microbialite formation and subsequent processes. Our understanding of this record is still limited by an incomplete knowledge of the macro‐ and mesoscale morphotypes of microbialites, along with their spatial distribution and correlation with microbial and geochemical processes that influence microbialite formation. In this study, we investigated the spatial distribution, morphotypes, mineralogy, geochemistry, and microbial diversity of the microbialites and identified six distinct zones (Zone I to Zone VI) with major microbialite build‐ups in Lake Salda. Newly identified microbialites were classified based on the macro‐ and mesostructures. Our work shows that the lake contains stromatolites, thrombolites, stromatolitic thrombolites, dendrolites, and microbially induced sedimentary structures. At macroscale, Lake Salda microbialites exhibit hemispheres, stacked domes, and laterally linked columnar structures while minicolumns, knobs, mesoclots, laminae, and botryoidal structures are common at mesoscale. The macro‐ and mesoscale distribution of different microbialite types spatially correlates with microbial community composition and water depth. Deep‐growing microbialites with a low abundance of Cyanobacteria (∼1%–4%) and high abundance of Firmicutes (28%–93%) exhibit steeply convex lamination, producing finger‐like minicolumnar mesostructures. In contrast, shallow‐growing microbialites with a low abundance of Firmicutes (0%–5%) and high abundance of Cyanobacteria (11%–37%) have well‐preserved gently convex millimeter‐scale lamination, resulting in cauliflower mesostructures. Palygorskite ((Mg, Al)2Si4O10(OH)) is identified in the diatom‐rich microbial layer of the deep‐growing microbialites. Regardless of the microbialite types, hydromagnesite and aragonite are present in the extracellular polymeric substance (EPS)‐rich zone of the shallow and deep‐growing microbialites. Overall, environmental changes (e.g., water depth and, accommodation space) play a major role in the formation and spatial distribution of different microbialite morphologies at the macro‐ and mesoscale. Differences in the relative abundance of dominant microorganisms between mesostructured types suggest that mesomorphology may be influenced by changes in microbial diversity. Spatial variations in the microbialite morphotypes, along with the abundant presence of entombed biomass (e.g., mineralized filaments), may indicate areas that have a high potential for the preservation of biosignatures.

Effects of Meyerozyma guilliermondii PJ15 on the biocontrol of Penicillium crustosum causing postharvest decay in Orah and its influence on the microbial diversity of Orah

Abstract Objectives Isolate biocontrol microorganisms that inhibit Penicillium crutosum, and explore their effects on the microbial control and microbial diversity change of Penicillium crustosum causing postharvest decay in Orah. Materials and Methods The biocontrol effect was verified by confrontation experiment. The microbial diversity was analyzed using high-throughput sequencing technology. Metabolomics analysis was performed using LC-MS/MS. Results a strain of Meyerozyma guilliermondii PJ15 that strongly inhibited Penicillium crustosum was isolated from grape surface, which could effectively inhibit the mycelium growth and green spore production of Penicillium crustosum. PJ15 could reduce the sourness and nutrient loss of Orah caused by Penicillium crutosum. Compared with the control, PJ15 treatment increased pH by 11.32%, soluble protein by 154.51%, ascorbic acid by 160.99%, and soluble total sugar by 203.53%. Microbial diversity analysis showed that PJ15 has a relatively small impact on the bacterial composition and diversity on the surface of Orah, but has a significant impact on the fungal composition and diversity. It can increase the fungal diversity of Orah invaded by Penicillium crustosum, increase the density of fungal interaction networks, and form a stronger coexisting survival interaction network. The vaccination of PJ15 downregulated differential metabolites 5,6-Epoxytetraene, which showed a positive correlation with Penicillium crustosum and a negative correlation with PJ15. Conclusions Meyerozyma guilliermondii PJ15 has a strong inhibitory effect on the growth of Penicillium crustosum, and has a significant impact on the fungal composition and diversity on the surface of Orah. It has the potential for biocontrol of Penicillium crustosum causing postharvest decay in Orah.

Impact of Transgenic Maize Ruifeng125 on Diversity and Dynamics of Bacterial Community in Rhizosphere Soil.

With the development of commercialized planting of genetically modified crops, their ecological security risks remain a key topic of public concern. Insect-resistant genetically modified maize, Ruifeng125, which expresses a fusion Bt protein (Cry1Ab-Cry2Aj), has obtained the application safety certificate issued by the Chinese government. To determine the effects of Ruifeng125 on the diversity and dynamics of bacterial communities, the accumulation and degradation pattern of the fusion Bt protein in the rhizosphere soil of transgenic maize were detected. Results showed that the contents of Bt protein varied significantly at different developmental stages, but after straw was returned to the field, over 97% of Bt proteins were degraded quickly at the early stages (≤10 d) and then they were degraded at a relatively slow rate. In addition, the variations in bacterial community diversity in the rhizosphere soil were detected by 16S ribosomal RNA (Rrna) high-throughput sequencing technology. A total of 44 phyla, 435 families, and 842 genera were obtained by 16S rRNA sequencing, among which Proteobacteria, Actinobacia, Acidobacter Acidobacterium, and Chloroflexi were the dominant taxa. At the same developmental stage, no significant differences in soil bacterial diversity were detected between Ruifeng125 and its non-transgenic control variety. Further analysis revealed that developmental stage, rather than the transgenic event, made the greatest contribution to the changes in soil microbial diversity. This research provides important information for evaluating the impacts of Bt crops on the soil microbiome and establishes a theoretical foundation for their environmental safety assessment.