Changes In Microbial Populations Research Articles

Diabetes and gut microbiome.

Diabetes mellitus represents a significant global health problem. The number of people suffering from this metabolic disease is constantly rising and although the incidence is heterogeneous depending on region, country, economic situation, lifestyle, diet and level of medical care, it is increasing worldwide, especially among youths and children, mainly due to lifestyle and environmental changes. The pathogenesis of the two most common subtypes of diabetes mellitus, type 1 (T1DM) and type 2 (T2DM), is substantially different, so each form is characterized by a different causation, etiology, pathophysiology, presentation, and treatment. Research in recent decades increasingly indicates the potential role of the gut microbiome in the initiation, development, and progression of this disease. Intestinal microbes and their fermentation products have an important impact on host metabolism, immune system, nutrient digestion and absorption, gut barrier integrity and protection against pathogens. This review summarizes the current evidence on the changes in gut microbial populations in both types of diabetes mellitus. Attention is focused on changes in the abundance of specific bacterial groups at different taxonomic levels in humans, and microbiome shift is also assessed in relation to geographic location, age, diet and antidiabetic drug. The causal relationship between gut bacteria and diabetes is still unclear, and future studies applying new methodological approaches to a broader range of microorganisms inhabiting the digestive tract are urgently needed. This would not only provide a better understanding of the role of the gut microbiome in this metabolic disease, but also the use of beneficial bacterial species in the form of probiotics for the treatment of diabetes.

Evaluating flow cytometric metrics for enhancing microbial monitoring in drinking water treatment processes

Evaluating flow cytometric metrics for enhancing microbial monitoring in drinking water treatment processes

Efficacy of Air and Oxygen Micro-nano Bubble Waters Against Colletotrichum gloeosporioides and Impacts on Postharvest Quality of 'Fan Retief' Guava Fruit.

This study focused on the application of micro-nano bubbles (MNBs) water generated using air or oxygen (O2), as an alternative to chlorine-based wash for fruits. For the in vitro and in vivo investigation, 106 spore or conidia/mL Colletotrichum gloeosporioides suspension was used, and treated with solutions of air- or O2-MNB for 30- or 60-min, sodium hypochlorite (NaOCl), and untreated (as control). In the second experiment, freshly harvested guava fruits were washed with tap water (control), NaOCl (standard practice), air-, or O2-MNB (for 15- or 30-min). All samples were packaged, stored for 21 days at 13 °C, and monitored for changes in natural microbial population and quality attributes. Based on the confocal laser and transmission electron microscopy results, exposure of C. gloeosporioides to air-MNB for 60 min resulted in the lowest viable cell count (%) compared to control and other treatments (O2-MNB and NaOCl). Air- and O2-MNB treatments damaged cellular structures, disrupted cell membrane integrity, and deformed hyphal morphology. Washing 'Fan Retief' guava (Psidium guajava L.) in air- or O2-MNB (for 15 and/or 30 min), better-retained tissue strength, delayed changes in color, and total soluble solid (TSS) content. Notably, MNB treatments were as effective as NaOCl washing and significantly reduced microbial load on fruit surface by ≥2 Log (p < 0.05). Micro-nano bubble water treatment offers a new paradigm for decontamination and preservation of guava fruit quality.

Study on volatile metabolites and microbial community in the fermentation process of black tea (Jiuqu hongmei tea)

Study on volatile metabolites and microbial community in the fermentation process of black tea (Jiuqu hongmei tea)

Bioplastic’s Valorisation by Anaerobic Co-Digestion with WWTP Mixed Sludge

Bioplastics are designed to degrade at the end of their lifecycle, but effective management of their end-of-life phase and integration into existing organic waste management systems remain significant challenges. Some bioplastics decompose under anaerobic conditions, with the anaerobic digestion (AD) process being a potential solution for their disposal. AD is a promising technology for valorising organic wastes, enabling biomethane production, reducing carbon footprints, and promoting product circularity. This study focuses on evaluating the continuous co-digestion of bioplastics with mixed sludge from an urban wastewater treatment plant (WWTP). Polyhydroxybutyrate (PHB) was the selected bioplastic, as various studies have reported its high and rapid degradation under anaerobic mesophilic conditions. PHB’s biodegradability under typical WWTP anaerobic digestion conditions (35 °C, 20-day retention time) was assessed in batch tests and the results indicate that PHB degradation ranged from 68 to 75%, depending on particle size. To further explore the potential of AD for PHB valorisation, the feasibility of anaerobic co-digestion of PHB with WWTP sludge was tested on a continuous laboratory scale using two digesters: a conventional digester (CSTR) and an anaerobic membrane bioreactor (AnMBR). The results indicated complete degradation of PHB, which led to higher biomethanisation percentages in both digesters, rising from 58% to 70% in the AnMBR and from 44% to 72% in the CSTR. The notable increase observed in the CSTR was attributed to changes in microbial populations that improved sludge biodegradability.

Microplastics in Farmed Animals—A Review

Environmental pollution from plastics has become one of the biggest concerns globally. Microplastics (MPs) are plastic materials less than 5 mm in size. They remain in the environment for hundreds to thousands of years without degrading, only breaking down further to nanoplastics (NPs). Micro- and nanoplastics can be the origin of many diseases and can carry various pathogenic substances on their surface and spread them throughout the biosphere, starting with contained additives and ending with adsorbed toxins from the environment and potentially pathogenic microorganisms. Exposure routes for humans and animals are through air, water and food/feed. Due to the placement of livestock—including ruminants, fish and poultry—and humans at the top of the food web, any pollution in water, air or soil can eventually be transferred to livestock and from livestock to humans. The presence of microplastics in the intestines of aquaculture species, ruminants and poultry, for instance, was found to cause a change in the intestinal microbial population and, as a result, the occurrence of diseases. These particles have also been observed in other organs such as liver, kidneys, lung, spleen, heart, ovaries, and testicles of animals, which causes biochemical changes, structural destruction, and malfunction. While the complete extent of the negative health impacts of microplastics remains still largely unknown, their ubiquitous presence and the transmission of chemicals from microplastics to organisms is a notable issue, underscoring the importance of gaining a more comprehensive understanding of the potential threats posed by microplastics to animal and ultimately human health, coupled with a need for drastic reduction of the plastic freight into the environment. This review article summarizes recent findings on the effect of micro- and nanoplastics on farmed animals and, ultimately, on humans. Action is needed to reduce the number of microplastics to which farmed animals, and thereby humans, are exposed.

Supercooled Storage Suppresses the Microbial Population and Color Changes in Fresh-Cut Cabbage

Supercooled Storage Suppresses the Microbial Population and Color Changes in Fresh-Cut Cabbage

Effects of yeast culture supplementation on milk yield, rumen fermentation, metabolism, and bacterial composition in dairy goats.

The effects of yeast culture (YC) on dairy goat milk yield and potential effects of rumen microbial population changes on rumen fermentation are poorly understood. This study aimed to evaluate the effects of YC on milk yield and rumen fermentation in dairy goats and explore the potential microbial mechanisms. Forty Laoshan dairy goats with a weight of 51.23 ± 2.23 kg and daily milk yield of 1.41 ± 0.26 kg were randomly divided into 4 groups: control (no YC), YC1 (10 g/day per goat), YC2 (25 g/day per goat), and YC3 (40 g/day per goat). The pre-feeding period was 15 days, and the official period was 60 days. Laoshan dairy goats were milked twice daily, and the individual milk yield was recorded. On the last day of the official period, rumen fluid was collected to measure rumen fermentation, perform quantitative polymerase chain reaction (PCR), and detect metabolites. Compared to the control group, the YC group had greater milk yield; higher acetic acid, butyric acid, and total volatile fatty acid contents; and lower ammonia-N (NH3-N) content in the rumen (p < 0.05). YC increased the abundance of Clostridia_UCG-014 and Paraprevotella (p < 0.05). Differential metabolites L-leucine and aspartic acid were screened. This study revealed the microbial mechanisms linking the relative abundance of Paraprevotella and Clostridia_UCG-014 to L-leucine and aspartic acid utilization. These results describe the potential benefits of supplementing 10 g/day per goat YC in the diets of Laoshan dairy goats for improving the rumen environment and milk yield.

Effect of long-term radish (Raphanus sativus var. sativus) monoculture practice on physiological variability of microorganisms in cultivated soil

Long-term monoculture may affect soil environment biodiversity. An example of such a plant is radish (Raphanus sativus var. sativus), an economically important crop in Poland, a quick-growing vegetable with intensified harvest throughout the season. The aim of this study was to determine changes in biodiversity of soil under radish cultivation and to compare the research methods applied. The monoculture practice affected soil pH, but the organic carbon content remained stable. 16S RNA-seq analysis revealed changes in soil microbial population, with the dominant phyla Proteobacteria (37.3%), Acidobacteria (19%), and Actinobacteria (16%), and the dominant taxa Gaiella (1.59%), Devosia (1.51%) and Nocardioides (1.43%). These changes have not fully expressed in the number of culturable microorganisms, where only fungal abundance changed significantly. However, the physiological state of microbial cells (λ) indicated that oligotrophs and copiotrophs were in a vegetative (λ>3.0) state at the beginning of the season and fungi at the end of the year. Changes in the biodiversity of soil microorganisms were visualised using Community Level Physiological Profiling, where an oscillation in Average Well Colour Development (OD560=0.78-1.48) was observed in successive months of radish culture, with biodiversity indices (Shannon and Substance richness) remaining similar. The greatest variation in the influence of monoculture practice on soil factors was observed for the soil enzymes activities (for dehydrogenase and peroxidase activities - 0.5μg TPF/h/g DW and 1.5 μmolPYGL/h/g DW respectively). Alkaline phosphatases predominated among this group of enzymes, and the activity of carbon metabolism enzymes decreased over the season, except for invertases, where an increase in activity of up to 50μg Glc/h/g DW was observed. All the parameters studied indicated changes in the soil environment. Nevertheless the microbial community remains stable during the whole experiment returning to equilibrium in a quite short time after changing conditions.

Changes in nitrogen functional genes and microbial populations in soil profiles of a peatland under different burning regimes

Changes in nitrogen functional genes and microbial populations in soil profiles of a peatland under different burning regimes

Multisite Field Evaluation of Bacteriophages for Fire Blight Management: Incorporation of Ultraviolet Radiation Protectants and Impact on the Apple Flower Microbiome.

Fire blight, a disease of pome fruits caused by the bacterium Erwinia amylovora, has become increasingly difficult to manage after the emergence of streptomycin-resistant strains. Alternative antibiotics and copper are available; however, these chemicals have use restrictions in some countries and also can carry risks of phytotoxicity. Therefore, there is growing interest in biological-based management options, with bacteriophage (phages) showing promise, as these naturally occurring pathogens of bacteria are easy to isolate and grow. However, there are several technical challenges regarding the implementation of phage biocontrol in the field, as the viral molecules suffer from ultraviolet radiation (UVR) degradation and can die off rapidly in the absence of the host bacterium. In this work, we assessed the efficacy of Erwinia phages and a commercial phage product for blossom blight control in the field across multiple locations in the eastern United States. In these tests, disease control ranged from 0.0 to 82.7%, and addition of a UVR protectant only resulted in significantly increased disease control in 2 of 12 tests. We also analyzed microbial community population changes in response to phage application. Changes in bacterial community diversity metrics over time were not detected; however, relative abundances of target taxa were temporarily reduced after phage applications, indicating that these phage applications did not have deleterious effects on the flower microbiome. We have demonstrated that biological control of fire blight with phages is achievable, but a better understanding of phage-pathogen dynamics is required to optimize disease control efficacy.

Biostimulation of sulfate reduction for in-situ metal(loid) precipitation at an industrial site in Flanders, Belgium

A 30-month pilot study was conducted to evaluate the potential of in-situ metal(loid) removal through biostimulation of sulfate-reducing processes. The study took place at an industrial site in Flanders, Belgium, known for metal(loid) contamination in soil and groundwater. Biostimulation involved two incorporations of an organic substrate (emulsified vegetable oil) as electron donor and potassium bicarbonate to raise the pH of the groundwater by 1-1.5units. The study focused on the most impacted permeable fine sand aquifer (8-9m below groundwater level) confined by layers of non-permeable clay. The fine sands exhibited initially oxic conditions (50-200mV), an acidic pH of 4.5 and sulfate concentrations ranging from 600 to 800mg/L. At the central monitoring well, anoxic conditions (-200 to -400mV) and a pH of 5.9 established shortly after the second substrate and reagent injection. Over the course of 12months, there was a significant decrease in the concentration of arsenic (from 2500 to 12μg/L), nickel (from 360 to <2μg/L), zinc (from 78,000 to <2μg/L), and sulfate (from 930 to 450mg/L). Low levels of metal(loid)s were still present after 34months (end of study). Mineralogical analysis indicated that the precipitates formed were amorphous in nature. Evidence for biologically driven metal(loid) precipitation was provided by compound specific stable isotope analysis of sulfate. In addition, changes in microbial populations were assessed using next-generation sequencing, revealing stimulation of native sulfate-reducing bacteria. These results highlight the potential of biostimulation for long-term in situ metal(loid) plume treatment/containment.

Aryl hydrocarbon receptor activity in intestinal epithelial cells in the formation of colonic tertiary lymphoid tissues.

After birth, the development of secondary lymphoid tissues (SLTs) in the colon is dependent on the expression of the aryl hydrocarbon receptor (AhR) in immune cells as a response to the availability of AhR ligands. However, little is known about how AhR activity from intestinal epithelial cells (IECs) may influence the development of tertiary lymphoid tissues (TLTs). As organized structures that develop at sites of inflammation or infection during adulthood, TLTs serve as localized centers of adaptive immune responses, and their presence has been associated with the resolution of inflammation and tumorigenesis in the colon. Here, we investigated the effect of the conditional loss of AhR activity in IECs in the formation and immune cell composition of TLTs in a model of acute inflammation. In females, loss of AhR activity in IECs reduced the formation of TLTs without significantly changing disease outcomes or immune cell composition within TLTs. In males lacking AhR expression in IECs, increased disease activity index, lower expression of functional-IEC genes, increased number of TLTs, increased T-cell density, and lower B- to T-cell ratio were observed. These findings may represent an unfavorable prognosis when exposed to dextran sodium sulfate (DSS)-induced epithelial damage compared with females. Sex and loss of IEC AhR also resulted in changes in microbial populations in the gut. Collectively, these data suggest that the formation of TLTs in the colon is influenced by sex and AhR expression in IECs.NEW & NOTEWORTHY This is the first research of its kind to demonstrate a clear connection between biological sex and the development of tertiary lymphoid tissues (TLT) in the colon. In addition, the research finds that in a preclinical model of inflammatory bowel disease, the expression of the aryl hydrocarbon receptor (AhR) influences the development of these structures in a sex-specific manner.

Colonic in vitro fermentation of mycoprotein promotes shifts in gut microbiota, with enrichment of Bacteroides species

Mycoprotein is a fungal-derived ingredient used for meat alternative products whose fungal cell walls are rich in dietary fibre (β-glucans and chitin) and defines its structure. Several health benefits have been reported after mycoprotein consumption, however, little is known about the impact of mycoprotein fermentation on the gut microbiota. This study aims to identify changes in microbiome composition and microbial metabolites during colonic fermentation of mycoprotein following simulated upper gastrointestinal digestion. Changes in microbial populations and metabolites produced by the fermentation of mycoprotein fibre were investigated and compared to a plant (oat bran) and an animal (chicken) comparator. In this model fermentation system, mycoprotein and oat showed different but marked changes in the microbial population compared to chicken, which showed minimal differentiation. In particular, Bacteroides species known for degrading β-glucans were found in abundance following fermentation of mycoprotein fibre. Mycoprotein fermentation resulted in short-chain fatty acid production comparable with oat and chicken at 72 h. Significantly higher branched-chain amino acids were observed following chicken fermentation. This study suggests that the colonic fermentation of mycoprotein can promote changes in the colonic microbial profile. These results highlight the impact that the unique structure of mycoprotein can have on digestive processes and the gut microbiota.

Food additives impair gut microbiota from healthy individuals and IBD patients in a colonic in vitro fermentation model

Intestinal fibrosis is a long-term complication of inflammatory bowel diseases (IBD). Changes in microbial populations have been linked with the onset of fibrosis and some food additives are known to promote intestinal inflammation facilitating fibrosis induction. In this study, we investigated how polysorbate 80, sucralose, titanium dioxide, sodium nitrite and maltodextrin affect the gut microbiota and the metabolic activity in healthy and IBD donors (patients in remission and with a flare of IBD). The Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) with a static (batch) configuration was used to evaluate the effects of food additives on the human intestinal microbiota. Polysorbate 80 and sucralose decreased butyrate-producing bacteria such as Roseburia and Faecalibacterium prausnitzii. Both compounds, also increased bacterial species positively correlated with intestinal inflammation and fibrosis (i.e.: Enterococcus, Veillonella and Mucispirillum schaedleri), especially in donors in remission of IBD. Additionally, polysorbate 80 induced a lower activity of the aryl hydrocarbon receptor (AhR) in the three groups of donors, which can affect the intestinal homeostasis. Maltodextrin, despite increasing short-chain fatty acids production, promoted the growth of Ruminococcus genus, correlated with higher risk of fibrosis, and decreased Oscillospira which is negatively associated with fibrosis. Our findings unveil crucial insights into the potential deleterious effects of polysorbate 80, sucralose and maltodextrin on human gut microbiota in healthy and, to a greater extent, in IBD patients.

Microbial entropy change and external dissipation process of urban sewer ecosystem.

As the initial stage of the sewage treatment system, the degradation of pollutants inevitably involves an entropy change process. Microorganisms play a vital role, where they interact with pollutants and constantly adjust own ecosystem. However, there is a lack of research on the entropy change and external dissipation processes within the sewer system. In this study, considering the characteristics of microbial population changes in the biofilm within the urban sewage pipe network, entropy theory is applied to characterize the attributes of different microorganisms. Through revealing the entropy change of the microbial population and chemical composition, a coupling relationship between the functional bacteria diversity, organic substances composition, and external dissipation in the pipeline network is proposed. The results show that the changes of nutrient availability, microbial community structure, and environmental conditions all affect the changes of information entropy in the sewer network. This study is critical for assessing the understanding of ecological dynamics and energy flows within these systems and can help researchers and operation managers develop strategies to optimize wastewater treatment processes, mitigate environmental impacts, and promote sustainable management practices.

Appraisal of Visible/IR and microwave datasets for land surface fluxes estimation using machine learning techniques

Appraisal of Visible/IR and microwave datasets for land surface fluxes estimation using machine learning techniques

Control of odorants in swine manure and food waste co-composting via zero-valent iron /H2O2 System

Odors have posed challenges to the advancement of aerobic composting. This work aims to identify the primary components responsible for odors and assess the effectiveness and mechanisms of the zero-valent iron/H2O2 system controlling various odorants in aerobic composting. Swine manure and food waste were used as composting materials, with the addition of zero-valent iron and hydrogen peroxide to mitigate odor emissions. Results revealed that odorants included ammonia, hydrogen sulfide, and 22 types of volatile organic compounds (VOCs), with ethyl acetate, heptane, and dimethyl disulfide being predominant. Among the odorants emitted, ammonia accounted for 75.43%, hydrogen sulfide for 0.09%, and identified VOCs for 24.48%. The ZVI/H2O2 system showed a significant reduction in ammonia and VOCs emission, with the reduction of 51% (ammonia) and 41.3% (VOCs) respectively, primarily observed during the thermophilic period. The occurrence of Fenton-like reactions and changes in key microbial populations were the main mechanisms accounting for odor control. The occurrence of Fenton-like reaction was confirmed by X-ray photoelectron spectroscopy and reactive oxygen detection, showing the oxidation of zero-valent iron by H2O2 to higher valence elemental iron, and the simultaneous production of ·OH. Microbial analysis indicated that an enrichment of specific microorganisms with Bacillus contributed to feammonx and Bacillaceae contributed to organic biodegradation. Redundancy analysis highlighted the role of key microbial species (Bacillaceae, Bacillus, and Ureibacillus) in effectively reducing the level of ammonia and volatile organic compounds. These novelty findings illustrated that the potential of this system is promising for controlling the emission of odorants and aerobic composting reinforcement.

Early Developmental Exposure to Triclosan Impacts Fecal Microbial Populations, IgA and Functional Activities of the Rat Microbiome.

Triclosan (TCS), a broad-spectrum antibacterial chemical, is detected in human urine, breast milk, amniotic fluid, and feces; however, little is known about its impact on the intestinal microbiome and host mucosal immunity during pregnancy and early development. Pregnant female rats were orally gavaged with TCS from gestation day (GD) 6 to postpartum (PP) day 28. Offspring were administered TCS from postnatal day (PND) 12 to 28. Studies were conducted to assess changes in the intestinal microbial population (16S-rRNA sequencing) and functional analysis of microbial genes in animals exposed to TCS during pregnancy (GD18), and at PP7, PP28 and PND28. Microbial abundance was compared with the amounts of TCS excreted in feces and IgA levels in feces. The results reveal that TCS decreases the abundance of Bacteroidetes and Firmicutes with a significant increase in Proteobacteria. At PND28, total Operational Taxonomic Units (OTUs) were higher in females and showed correlation with the levels of TCS and unbound IgA in feces. The significant increase in Proteobacteria in all TCS-treated rats along with the increased abundance in OTUs that belong to pathogenic bacterial communities could serve as a signature of TCS-induced dysbiosis. In conclusion, TCS can perturb the microbiome, the functional activities of the microbiome, and activate mucosal immunity during pregnancy and early development.

Metaproteomics analysis of anaerobic digestion of food waste by the addition of calcium peroxide and magnetite.

Adding trace calcium peroxide and magnetite into a semi-continuous digester is a new method to effectively improve the anaerobic digestion of food waste. However, the microbial mechanism in this system has not been fully explored. Metaproteomics further revealed that the most active and significantly regulated genus u_p_Chloroflexi had formed a good cooperative relationship with Methanomicrobiales and Methanothrix in the system. u_p_Chloroflexi decomposed more organic compounds into CO2, acetate, amino acids, and other substances by alternating between short aerobic-anaerobic respiration. It perceived and adapted to the surrounding environment by producing biofilm, extracellular enzymes, and accelerating substrate transport, formed a respiratory barrier, and enhanced iron transport capacity by using highly expressed cytochrome C. The methanogens formed reactive oxygen species scavengers and reduced iron transport to prevent oxidative damage. This study provides new insight for improving the efficiency of anaerobic digestion of food waste and identifying key microorganisms and their regulated functional proteins in the calcium peroxide-magnetite digestion system.IMPORTANCEPrevious study has found that the combination of calcium peroxide and magnetite has a good promoting effect on the anaerobic digestion process of food waste. Through multiple omics approaches, information such as microbial population structure and changes in metabolites can be further analyzed. This study can help researchers gain a deeper understanding of the digestion pathway of food waste under the combined action of calcium peroxide and magnetite, further elucidate the impact mechanisms of calcium peroxide and magnetite at the microbial level, and provide theoretical guidance to improve the efficiency and stability of anaerobic digestion of food waste, as well as reduce operational costs. This research contributes to improving energy recovery efficiency, promoting sustainable management and development of food waste, and is of great significance to environmental protection.