Decrease In Microbial Diversity Research Articles

The Impact of High Temperature on Microbial Communities in Pork and Duck Skin.

Pork skin and duck skin are highly favored by consumers in China, and high-temperature processing methods are widely employed in cooking and food preparation. However, the influence of high-temperature treatment on the microbial communities within pork skin and duck skin remains unclear. In this study, a high-temperature treatment method simulating the cooking process was utilized to treat samples of pork skin and duck skin at temperatures ranging from 60 °C to 120 °C. The findings revealed that high-temperature treatment significantly altered the microbial communities in both pork skin and duck skin. Heat exposure resulted in a decrease in microbial diversity and induced changes in the relative abundance of specific microbial groups. In pork skin, high-temperature treatment led to a reduction in bacterial diversity and a decline in the relative abundance of specific bacterial taxa. Similarly, the relative abundance of microbial communities in duck skin also decreased. Furthermore, potential pathogenic bacteria, including Gram-positive and Gram-negative bacteria, as well as aerobic, anaerobic, and facultative anaerobic bacteria, exhibited different responses to high-temperature treatment in pork skin and duck skin. These findings highlighted the substantial impact of high-temperature processing on the composition and structure of microbial communities in pork skin and duck skin, potentially influencing food safety and quality. This study contributed to an enhanced understanding of the microbial mechanisms underlying the alterations in microbial communities during high-temperature processing of pork skin and duck skin, with significant implications for ensuring food safety and developing effective cooking techniques.

Heart failure stimulates colorectal tumour growth through gut microbial alterations of specific populations

Abstract Background/purpose The field of reverse cardio-oncology has received growing attention in the last years, since epidemiological studies showed that patients with HF are at increased risk of developing cancer. In addition, HF can stimulate tumour growth directly in distant organs, including colon cancer. The exact mechanisms underlying this phenomenon, however, remain largely unknown. The connection between the microbiome and colorectal cancer (CRC) has been studied extensively and microbial dysbiosis in CRC is linked to cancer progression. Recent studies have also shown that HF patients display microbial dysbiosis. We hypothesized that microbial dysbiosis might contribute to HF-induced CRC tumour growth. Methods C57BL/6J mice were subjected to myocardial infarction (MI), with sham surgery as control. After six weeks faeces were collected, processed for 16s rRNA sequencing, and pooled for faecal microbial transplantation. CRC tumour growth was provoked in germ-free mice by treating them with Azoxymethane (AOM)/Dextran sodium sulphate (DSS). The CRC mice were transplanted with faeces from MI or sham mice. Disease progression was monitored using the disease severity score and endoscopy. After ten weeks mice were sacrificed, and tumour number and proliferation were quantified. All experimental procedures were performed in accordance with the European Union guidelines (CCD_8141, the Netherlands, LA_1400637, Belgium). Results MI-induced HF resulted in a decrease in microbial diversity (Shannon diversity p=0.018), characterized by a decrease in short chain fatty acid-producing bacteria, including the genera Blautia (p<0.01) and Roseburia (p<0.01). In addition, caecal butyrate levels were decreased in MI mice (p=0.029). These changes were largely comparable to microbial changes observed in HF patients and CRC patients. Interestingly, faecal transplantation with faeces from MI mice resulted in faster growth of CRC tumours in mice treated with AOM/DSS. This was demonstrated by a higher endoscopy score (7.9 ±2.5 vs. 10 ±2.4, p=0.038), indicative of worse disease progression, increased tumour counts (22 ±5.3 vs. 29 ±6, p<0.01), and a higher percentage of Ki67 positive cells in tumour tissue (p=0.012), relative to AOM/DSS treated mice transplanted with faeces from sham mice. Sequencing data revealed several differences in the microbial composition of mice transplanted with faeces from MI mice compared to mice transplanted with faeces from sham mice. Conclusion Our results demonstrate that HF induces microbial dysbiosis in mice. In addition, we show, for the first time, using a faecal transplantation model, that HF-induced microbial dysbiosis is causally involved in CRC tumour growth in a mouse model of CRC. Targeting the microbiome may present a tool to mitigate HF associated co-morbidities, especially cancer.Graphical abstract

Alterations in the intestinal microbiota associated with active tuberculosis and latent tuberculosis infection

ObjectivesTo study the characteristics of intestinal microbiota at different stages of Mycobacterium tuberculosis infection. MethodsFecal samples of 19 active tuberculosis (ATB) patients, 21 latent tuberculosis infection (LTBI) individuals, and 20 healthy controls (HC) were collected. Gut microbiota of all the participants were analyzed by 16S rDNA sequencing. Clinical information of ATB patients was also collected and analyzed. ResultsBoth ATB and LTBI groups showed significant decreases in microbial diversity and decline of Clostridia. For ATB patients, bacteria within phylum Proteobacteria increased. While for LTBI individuals, genera Prevotella and Rosburia enriched. The abundance of Faecalibacterium, Clostridia and Gammaproteobacteria has the potential to diagnose ATB, with the area under the curve (AUC) of 0.808, 0.784 and 0.717. And Prevotella and Rosburia has the potential to diagnose LTBI, with the AUC of 0.689 and 0.689. Notably, in ATB patients, the relative abundance of Blautia was negatively correlated with the proportions of peripheral T cells and CD8+T cells. And serum direct bilirubin was positively correlated with Bacteroidales, while negatively correlated with Clostridiales in ATB patients. ConclusionsThe specifically changed bacteria are promising markers for ATB and LTBI diagnosis. Some gut bacteria contribute to anti-MTB immunity through interactions with T cells and bilirubin.

Impact on the microbial population during biological volatile fatty acid production from olive mill solid waste

Volatile fatty acids (VFAs) revalorisation from waste products are key in achieving industrial sustainability and circular economic goals. Hence, the objective of this work was to correlate the adaptability of the microbial community in olive mill solid waste (OMSW) anaerobic fermentation processes, to the production of VFAs under different pH conditions, i.e. under acidic (pH 4 &5), neutral (pH 6 & 7) and alkaline conditions (pH 9 & 10). At neutral conditions, anaerobic digestion exhibited minimal accumulation of VFAs, as they were primarily biotransformed to methane, where no significant changes in the microbial community were observed. At acidic conditions, a diverse profile of VFAs were present in the reactors, although the VFA production was limited to around 20 % of fed OMSW. Despite the low accumulation, the VFA profile at pH 5 was more complex than those at alkaline conditions, accounting propionic acid as the main VFA compound produced at pH 5 (60 % of the total VFAs). Acidic conditions entailed a shift in the microbial composition compared to the initial inoculum, although the reactors maintained similar diversity indices. At alkaline conditions, around 50 % of the fed OMSW was accumulated as VFAs, mainly as acetic acid. Overall, a lower diversity and higher dominance corresponded to a less diverse VFAs profile, such as the preponderance of acetic acid correlated with a microbial diversity decrease and the increased dominance of Tissirella.

Skin microbiome in autoimmune pemphigus: a comparative analysis of bacterial diversity in relation to treatment

Background. Autoimmune pemphigus (AP) is a chronic, life-threatening disease of the skin and mucous membranes. Effective therapeutic options are currently available, but mortality in AP patients is higher than in the general population. The leading causes of death are infectious complications. Recent years have revealed the key role of microbiome alteration in a number of skin diseases. There is an increasing number of published studies examining the skin microbiome in patients with AP, but they have a number of limitations and require further research to understand the role of skin microbial composition in the course of AP. Aims: to study the composition of skin microbiome by culture method in patients with AP (in active stage and in remission), to perform correlation analysis of microbiome composition and therapy received. Materials and methods. Experimental prospective comparative study. Forty-four patients with diagnosed AP (16 men, 36.4%; 28 women, 63.6%; mean age 51.5±13.1 years) and 10 controls (7 women, 70%; 3 men, 30%; mean age 40±12.5 years) were included. Patients were enrolled between November 2021 and June 2023 at the V.A. Rakhmanov Clinic of Skin and Venereal Diseases. Results. Seventy-nine skin samples were obtained and analysed. Only bacterial growth was detected in all submitted samples. No statistically significant difference was found between the composition of the microbiome of the unchanged skin of patients with AP in the active stage and in remission and the control group. In patients in the active stage of AP, a significant difference was found between the composition of the microbiome from rash elements and unchanged skin. S. aureus prevails on the skin from rash elements, and S. hominis dominates on unchanged skin. In patients before the start of glucocortlcosteroid (GCS) therapy, a predominance of S. aureus in the samples and a decrease in microbial diversity is noted. In patients receiving GCS therapy, S. hominis and S. epidermidis predominate, and greater microbial diversity is also noted. Conclusions. The study revealed that the skin microbiome from the rash elements of patients with AP undergoes significant changes during the active stage of the disease, mainly due to colonisation of the skin by S. aureus. However, against the background of therapy with systemic GCS there is a tendency to normalisation of skin microflora composition, which demonstrates that there are no differences in the composition of the microbiome of patients in remission of AP and control groups.

Responses of a Submerged Macrophyte Potamogeton crispus and Epiphytic Biofilm to Humic-Substance Enrichment Coupled with Brownification in Freshwater Habitats

Brownification denotes increasing water color, partly caused by increasing dissolved organic matter of terrestrial origin in freshwater. Brownification has become a wide-spread environmental problem because water color alters the physicochemical environment and biological communities in aquatic ecosystems. However, our understanding of its ecological effects on aquatic macrophytes is limited. Here, an indoor mesocosm experiment with a common submerged macrophyte, Potamogeton crispus, along an increasing gradient of brownification was conducted over a period of 42 days. Results showed that P. crispus was able to overcome low degrees of brownification owing to the plasticity in morphological and physiological traits and P. crispus growth even benefitted from the concomitant nutrients along with brownification. However, the macrophyte growth was negatively affected by a 10-fold increase in water color beyond its current level. Additionally, collapse in antioxidant systems and potent photosynthesis inhibition implied that P. crispus could not adapt to the low-light stress generated under the high degree of brownification. Epiphytic bacteria are more sensitive to brownification than their hosts. Any degree of brownification initially caused a decrease in microbial diversity of epiphytic biofilm, whereafter the concomitant nutrients under brownification favored the growth of epiphytic microorganisms. The shading effect of a large number of epiphytic biofilms under brownification may further aggravate the low-light stress on macrophytes. Overall, the study provides new insights into the comprehensive effects and underlying mechanisms of brownification on macrophytes.

Linking soil depth to aridity effects on soil microbial community composition, diversity and resource limitation

With ongoing climate change, aridity is increasing worldwide, affecting biodiversity and ecosystem function in drylands. However, how the depth-profile microbial community structure and metabolic limitations change along aridity gradients are still poorly explored. Here, 16S rRNA and ITS amplicon sequencing and ecoenzymatic stoichiometry analysis were used to investigate both bacterial and fungal diversities and resource limitations in 1 m depth profiles across a wide aridity gradient (0.51–0.78) in a semiarid region. Results showed a sharp decrease in microbial diversity with soil depth, accompanied by an increase in microbial phosphorus (P) vs. N (nitrogen) limitation and a decrease in microbial carbon (C) vs. nutrient limitation. Aridity led to a strong shift in microbial community composition, but aridity has a threshold effect on microbial resource limitation through impacts on soil pH and C/P or N/P. When the aridity threshold (1-precipitation/evapotranspiration) exceeds 0.65, relationship between aridity and microbial resource demand was decoupled; but at aridity threshold = 0.65, microbial relative C limitation and C-acquiring enzyme activity dropped. These results suggest that aridity might have a stronger influence on microbial community composition, than on diversity, shaped by inherent soil biotic factors (i.e., MBC:MBP or MBN:MBP). These findings suggest that soil microbial diversity or enzymatic stoichiometry may be not necessary to mirror changes in water availability in the drylands, while aridity would be well explained by microbial community composition.

Long-term effects of chloropicrin fumigation on soil microbe recovery and growth promotion of Panax notoginseng.

Panax notoginseng is a precious Chinese medicinal material. Soil fumigation can control soil-borne disease and overcome the continuous cropping obstacles of P. notoginseng. However, chloropicrin (CP) fumigation can kill non-target soil microorganisms and reduce microbial diversity, but the long-time impacts of CP fumigation on soil microbial are less reported. We studied the long-term effects of CP fumigation on soil microbes with high-throughput gene sequencing, and correlated the changes in the composition of microbial communities with environmental factors like soil physicochemical properties and soil enzyme activities. This study mainly focuses on the recovery characteristics of soil microbe after soil fumigation by evaluating the ecological restoration of P. notoginseng soil, its sustained control effect on plant diseases, and its promotion effect on crop growth by focusing on the CP fumigation treatment. The results showed that CP fumigation significantly increased soil available phosphorus (P) to 34.6 ~ 101.6 mg/kg and electrical conductivity (EC) by 18.7% ~ 34.1%, respectively. High-throughput gene sequencing showed that soil fumigation with CP altered the relative abundance of Trichoderma, Chaetomium, Proteobacteria, and Chloroflexi in the soil while inhibiting a lot of Fusarium and Phytophthora. The inhibition rate of Phytophthora spp. was still 75.0% in the third year after fumigation. Fumigation with CP enhanced P. notoginseng's survival rate and stimulated plant growth, ensuring P. notoginseng's healthy in the growth period. The impact of fumigation on microbial community assembly and changes in microbial ecological niches were characterized using normalized stochasticity ratio (NST) and Levins' niche breadth index. Stochasticity dominated bacterial community assembly, while the fungal community was initially dominated by stochasticity and later by determinism. Fumigation with CP reduced the ecological niches of both fungi and bacteria. In summary, the decrease in microbial diversity and niche caused by CP fumigation could be recovered over time, and the control of soil pathogens by CP fumigation remained sustainable. Moreover, CP fumigation could overcome continuous cropping obstacles of P. notoginseng and promote the healthy growth of P. notoginseng.

Mechanisms by which chloropicrin fumigation promotes soil potassium conversion and absorption.

Fumigation of soil using chloropicrin has been proven to significantly affect soil nutrient cycling, but the mechanism by which soil potassium conversion and plant uptake is promoted remains unclear. In this study, we conducted a fumigation experiment to investigate the effects of chloropicrin soil fumigation on the conversion of soil potassium post-fumigation (days 7-70), and its mechanisms, tomatos were planted in fumigated and non-fumigated soils to enable further comparisons. Results showed that the content of rapidly available potassium and available potassium decreased by 16-24% and 17-23% at day 28 respectively, when tomato was planted in chloropicrin-fumigated soils compared to the non-fumigated soils. The potassium content of tomato planted in fumigated soil was significantly higher than that planted in non-fumigated soil (30.3 vs. 21.9 mg g-1 dry weight). Chloropicrin fumigation resulted in a significant change in the soil bacterial and fungal community structures, and trigged a long-term (at least 70-day) decrease in microbial diversity. Network analysis showed that chloropicrin soil fumigation changed microbial co-occurrence patterns by decreasing bacterial total links, nodes, and average degree, and increasing fungal total links, nodes, and average degree. Chloropicrin fumigation caused significant changes in the relative abundance of Bacillus species, which are involved in potassium dissolution. Structural equation model (SEM) suggested that fumigation with chloropicrin enhanced the contribution of soil potassium to tomato growth and reduced the contribution of bacterial communities. Together, the results of our study help in understanding the crop yield enhancement mechanism of soil fumigation.

Microbiome-Gut-Mucosal-Immune-Brain Axis and Autism Spectrum Disorder (ASD): A Novel Proposal of the Role of the Gut Microbiome in ASD Aetiology.

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder characterised by deficits in social interaction and communication, as well as restricted and stereotyped interests. Due of the high prevalence of gastrointestinal disorders in individuals with ASD, researchers have investigated the gut microbiota as a potential contributor to its aetiology. The relationship between the microbiome, gut, and brain (microbiome-gut-brain axis) has been acknowledged as a key factor in modulating brain function and social behaviour, but its connection to the aetiology of ASD is not well understood. Recently, there has been increasing attention on the relationship between the immune system, gastrointestinal disorders and neurological issues in ASD, particularly in relation to the loss of specific species or a decrease in microbial diversity. It focuses on how gut microbiota dysbiosis can affect gut permeability, immune function and microbiota metabolites in ASD. However, a very complete study suggests that dysbiosis is a consequence of the disease and that it has practically no effect on autistic manifestations. This is a review of the relationship between the immune system, microbial diversity and the microbiome-gut-brain axis in the development of autistic symptoms severity and a proposal of a novel role of gut microbiome in ASD, where dysbiosis is a consequence of ASD-related behaviour and where dysbiosis in turn accentuates the autistic manifestations of the patients via the microbiome-gut-brain axis in a feedback circuit.

Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum-dominated bog.

Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.

Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China.

Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO4-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO4·HCO3-Ca·Mg to SO4-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.

Alteration of the Respiratory Microbiome in Hospitalized Patients with Asthma-COPD Overlap during and after an Exacerbation.

The immediate aim of this study was to comparatively examine the bacterial respiratory microbiome of patients in a stable state and during an exacerbation of asthma-COPD (chronic obstructive pulmonary disease) overlap (ACO). This prospective observational study took place in Jordan between 1 September 2021 and 30 April 2022. Sputum samples from patients with recognized ACO were acquired within 48 h of the exacerbation onset and again at 3 weeks following the exacerbation. The next-generation sequencing Illumina MiSeq was employed and uncovered significantly high bacterial diversity in the sputa. The results showed a significant decrease in the taxonomic richness in the sputum samples collected during the exacerbation episodes compared with those collected from patients in a stable state (p = 0.008), with an increase in the taxonomic evenness (p < 0.005). This change in the composition of the airway bacterial community suggests that the replacement of a significant portion of the airway microbiome with certain microorganisms may play a role in the decrease in microbial diversity observed during an ACO exacerbation. Greater knowledge of this link could allow for a more focused administration of antibiotics, especially during exacerbations, improving clinical efficacy and patient outcomes.

Changes in upper airways microbiota in ventilator-associated pneumonia

BackgroundThe role of upper airways microbiota and its association with ventilator-associated pneumonia (VAP) development in mechanically ventilated (MV) patients is unclear. Taking advantage of data collected in a prospective study aimed to assess the composition and over-time variation of upper airway microbiota in patients MV for non-pulmonary reasons, we describe upper airway microbiota characteristics among VAP and NO-VAP patients.MethodsExploratory analysis of data collected in a prospective observational study on patients intubated for non-pulmonary conditions. Microbiota analysis (trough 16S-rRNA gene profiling) was performed on endotracheal aspirates (at intubation, T0, and after 72 h, T3) of patients with VAP (cases cohort) and a subgroup of NO-VAP patients (control cohort, matched according to total intubation time).ResultsSamples from 13 VAP patients and 22 NO-VAP matched controls were analyzed. At intubation (T0), patients with VAP revealed a significantly lower microbial complexity of the microbiota of the upper airways compared to NO-VAP controls (alpha diversity index of 84 ± 37 and 160 ± 102, in VAP and NO_VAP group, respectively, p-value < 0.012). Furthermore, an overall decrease in microbial diversity was observed in both groups at T3 as compared to T0. At T3, a loss of some genera (Prevotella 7, Fusobacterium, Neisseria, Escherichia–Shigella and Haemophilus) was found in VAP patients. In contrast, eight genera belonging to the Bacteroidetes, Firmicutes and Fusobacteria phyla was predominant in this group. However, it is unclear whether VAP caused dysbiosis or dysbiosis caused VAP.ConclusionsIn a small sample size of intubated patients, microbial diversity at intubation was less in patients with VAP compared to patients without VAP.

Effects of Florfenicol on Intestinal Histology, Apoptosis and Gut Microbiota of Chinese Mitten Crab (Eriocheir sinensis).

Excessive use of antibiotics in aquaculture causes residues in aquatic animal products and harms human health. However, knowledge of florfenicol (FF) toxicology on gut health and microbiota and their resulting relationships in economic freshwater crustaceans is scarce. Here, we first investigated the influence of FF on the intestinal health of Chinese mitten crabs, and then explored the role of bacterial community in FF-induced intestinal antioxidation system and intestinal homeostasis dysbiosis. A total of 120 male crabs (48.5 ± 4.5 g) were experimentally treated in four different concentrations of FF (0, 0.5, 5 and 50 μg/L) for 14 days. Responses of antioxidant defenses and changes of gut microbiota were assessed in the intestine. Results revealed that FF exposure induced significant histological morphology variation. FF exposure also enhanced immune and apoptosis characteristics in the intestine after 7 days. Moreover, antioxidant enzyme catalase activities showed a similar pattern. The intestinal microbiota community was analyzed based on full-length 16S rRNA sequencing. Only the high concentration group showed a marked decrease in microbial diversity and change in its composition after 14 days of exposure. Relative abundance of beneficial genera increased on day 14. These findings illustrate that exposure to FF could cause intestinal dysfunction and gut microbiota dysbiosis in Chinese mitten crabs, which provides new insights into the relationship between gut health and gut microbiota in invertebrates following exposure to persistent antibiotics pollutants.

Modulation of the porcine intestinal microbiota in the course of Ascaris suum infection

BackgroundThe porcine roundworm Ascaris suum impairs feed conversion and weight gain, but its effects on intestinal microbiota remain largely unexplored.MethodsModulation of the intestinal microbiota was assessed in pigs that were infected once with 10,000 A. suum eggs and pigs that received a trickle infection (1000 eggs/day over 10 days), compared with a non-infected control group. Six pigs each were sacrificed per group at days 21, 35 and 49 post-infection (p.i.). Faecal samples taken weekly until slaughter and ingesta samples from different intestinal compartments were subjected to next-generation sequencing of the bacterial 16S rRNA gene.ResultsThe results revealed marked differences between the single- and the trickle-infected group. Single infection caused a remarkable but transient decrease in microbial diversity in the caecum, which was not observed in the trickle-infected group. However, an increase in short-chain fatty acid-producing genera in the caecum on day 21 p.i., which shifted to a decrease on day 35 p.i., was common to both groups, possibly related to changes in excretory–secretory products following the parasite’s final moult. Faecal microbial interaction networks were more similar between the single-infected and control group than the trickle-infected group. In addition, a lower degree of similarity over time indicated that A. suum trickle infection prevented microbiota stabilization.ConclusionsThese different patterns may have important implications regarding the comparability of experimental infections with natural scenarios characterized by continuous exposure, and should be confirmed by further studies.Graphical

The Impact of Vairimorpha (Nosema) ceranae Natural Infection on Honey Bee (Apis mellifera) and Bee Bread Microbiota

Honey bees face new challenges, ranging from climate crisis to emerging pathogens such as Vairimorpha (Nosema) ceranae that synergistically cause a syndrome designated as colony collapse disorder (CCD). This study employed a metataxonomic approach in order to investigate if V. ceranae affects gut microbiota (bacteria and fungi) of adult A. mellifera honey bees as well as microbiota of bee bread (BB) stored in colonies demonstrating severe V. ceranae infection (spore counts &gt;2,500,000 per bee) as compared with colonies exhibiting very low spore counts (&lt;40,000 per bee). Alpha-diversity analysis revealed an overall decrease in microbial diversity reflected by number of observed unique operating taxonomic units (OTUs) regarding both bacteria and fungi in honey bee and ΒΒ samples. Further analysis demonstrated that Podosphaera spp. were absent in BB samples collected from colonies with high spore counts, while relative abundance of Blumeria spp. was significantly decreased. Interestingly, relative abundance of Rosenbergiella spp. was increased in BB samples collected from colonies with high spore counts. The reason for these findings remains elusive. Although further research is warranted, overall reduced microbial diversity and relative abundance of certain microbial groups may serve as biomarkers of colony collapse.

Major impacts of caving activities on cave microbial diversity: case study of Morca Cave, Turkey.

Some of microorganisms identified in cave ecosystems have been reported to play a permanent and strategic role for maintaining life of these environments. Human entrance into caves can induce some changes of cave physicochemical parameters which ultimately impacts the living organisms. In these facts, for the first time, Morca Cave was explored in a purpose to evaluate the impacts that can be caused by the human activities on microbial diversity in a limited period of time. Morca is a karts cave located in the Taşeli Plateau in the Middle Taurus mountains in Turkey. The first entrance into this cave was in 2018, and expeditors reached to - 500m. During the second expedition in 2019, a camp was established at the - 1040-m depth during 4days. In order to evaluate the human impacts in a new explored cave, this camping depth is chosen to be our studied area because it was its first entrance. Before the installation and at the end of the camp, sediments and surface samples were taken from different points of the camp area and around. Sequencing of 16s rRNA of each sample to isolate DNA by using the next-generation sequencing (NGS) method was performed. The profile of the microbial diversity before the camping revealed that the class Thermoplasmata was dominated the archaea group and Gammaproteobacteria and Alphaproteobacteria were the most dominant bacterial classes. After the camp, most studied sites were noted with a decrease of microbial diversity especially the previous cited classes strains. Bacteria belonging to Bacilli class have increased after the camp. Increase of bacteria that are belonging to Bacteroidia has also observed in the most active areas. This present study highlight how cave microbial diversity can respond to the human activities within a short period inside a closed cave. Furthermore, it may constitute a solid basis and support on the improvement of techniques for cave management and expedition planning for the conservation of cave nature.

Study on Microbial Community Structure and Soil Nitrogen Accumulation in Greenhouse Vegetable Fields with Different Planting Years

Soil microbial communities are an important part of the soil ecosystem in greenhouse vegetable fields, where ammonia-oxidising microorganisms play a key role in nitrogen conversion. The health and stability of the ecological environment of greenhouse vegetable fields are affected by the number of years of continuous cultivation. We used real-time PCR amplification and 16S rRNA gene sequencing to analyse the changes in soil microbial community structure and diversity in different planting years (0, 3, 9, and 13). The content of environmental factors increased with the increase of planting year; the NO3−-N content in the 0–20 cm soil layer showed a cumulative trend, peaking to 1290–1390 mg/kg in year 13. The abundance of operational taxonomic units (OTUs) in the microbial community gradually decreased, and the OTUs of 0–20 cm soil layer in year 13 decreased by 52.2% compared to year 0. The Shannon and Simpson indices indicated a substantial decrease in microbial diversity after year 9. The dominant phyla in the soil microbial community mainly included Firmicutes (23.6%), Actinobacteria (23.2%), Proteobacteria (17.6%), Crenarchaeota (83.4%), and Euryarchaeota (2.7%). Nitrosopumilus and Nitrososphaera in the ammonia-oxidising archaeal (AOA) community and Nitrolancea and Nitrospira in the ammonia-oxidising bacterial (AOB) community dominated the ammonia-oxidising microorganisms. With the increase in planting years in greenhouse vegetable fields, the structure of soil microbial community changed significantly, with soil biomass and diversity significantly decreasing in years 9 and 13. Reasonable fertilization and planting year would improve microbial activity and provide a basis for sustainable utilization and high-quality production in greenhouse vegetable fields.

The interplay between PCOS pathology and diet on gut microbiota in a mouse model

ABSTRACT The gut microbiome has been implicated in polycystic ovary syndrome (PCOS) pathophysiology. PCOS is a disorder with reproductive, endocrine and metabolic irregularities, and several studies report that PCOS is associated with a decrease in microbial diversity and composition. Diet is an important regulator of the gut microbiome, as alterations in macronutrient composition impact the balance of gut microbial communities. This study investigated the interplay between macronutrient balance and PCOS on the gut microbiome of control and dihydrotestosterone (DHT)-induced PCOS-like mice exposed to diets that varied in protein (P), carbohydrate (C) and fat (F) content. The amount of dietary P, C and F consumed significantly altered alpha (α) and beta (β) diversity of the gut microbiota of control and PCOS-like mice. However, α-diversity between control and PCOS-like mice on the same diet did not differ significantly. In contrast, β-diversity was significantly altered by PCOS pathology. Further analysis identified an operational taxonomic unit (OTU) within Bacteroides (OTU3) with 99.2% similarity to Bacteroides acidifaciens, which is inversely associated with obesity, to be significantly decreased in PCOS-like mice. Additionally, this study investigated the role of the gut microbiome in the development of PCOS traits, whereby PCOS-like mice were transplanted with healthy fecal microbiota from control mice. Although the PCOS gut microbiome shifted toward that of control mice, PCOS traits were not ameliorated. Overall, these findings demonstrate that while diet exerts a stronger influence over gut microbiota diversity than PCOS pathology, overall gut microbiota composition is affected by PCOS pathology.