16S rRNA Amplicon Research Articles

Comparing the effectiveness of different DNA extraction methods in MX-80 bentonite.

Approaches to DNA extraction play a crucial role in determining the variability of results obtained through 16S rRNA amplicon sequencing. Particularly, clay-rich samples can impede the efficiency of various standard cultivation-independent techniques. We conducted an inter-laboratory comparison study to thoroughly assess the efficacy of two published DNA extraction methods (kit-based and phenol-chloroform-based) specifically designed for bentonite samples. To this end, we spiked Wyoming MX 80 bentonite with two different mock communities and compared the obtained DNA yield and purity, the presence of contaminants and the community profile. Our findings suggest that both methods are equally viable, with the best choice depending on the specific requirements of the downstream analysis. However, it is crucial to maintain consistency in the chosen method, as comparing results becomes challenging, particularly in the presence of bentonite. In summary, our study emphasizes the significance of standardized DNA extraction methods and underscores the importance of validating these methods using appropriate controls when studying microbial communities with 16S rRNA amplicon sequencing, particularly in environments characterized by low biomass and clay-rich compositions. Additionally, slight modifications to one of the extraction methods can substantially enhance its efficiency.

Unveiling the mechanism underlying in−situ enhancement on anammox system by sulfide: Integration of biological and isotope analysis

The in−situ utilization of sulfide to remove the nitrate produced during the anaerobic ammonium oxidation (anammox) process can avoid prolonged sludge acclimatization, facilitating the rapid initiation of coupled nitrogen removal processes. However, the understanding of in−situ enhancement on anammox system by sulfide remains unclear. Herein, sulfide (Na2S) was introduced as an additional electron donor to remove the nitrate derived from the anammox under varying sulfide/nitrogen (S/N, S2−-S/NO3–-N, molar ratio) ratios (0.004–4.375). The underlying mechanisms were elucidated by molecular biology techniques including flow cytometry, quantitative polymerase chain reaction, and 16S rRNA amplicon sequencing, alongside isotope tracer analysis. Results revealed that anammox reactors, when operated with in−situ sulfide addition, exhibited a significant enhancement in total nitrogen removal efficiency (NRE) ranging from 11.5%−41.7% (achieved 96%), with the optimal S/N ratios of 0.01−0.8. Isotope tracer analysis indicated the successful coupling of the anammox, sulfur autotrophic denitrification (SADN), and dissimilatory nitrate reduction to ammonium (DNRA) processes within the system, with their contributions to nitrogen removal being 46%−50%, 24%−30%, and 20%−22%, respectively. Moreover, a notable increase in the abundance of sulfur–oxidizing bacteria (SOB) (20%−40% increase) and DNRA bacteria (10%−20% increase) were observed. Effective collaboration was further supported by the sustained viability of microbial communities. It is speculated that the heightened presence of SOB and DNRA bacteria created a low toxicity environment by converting sulfide to biogenic sulfur, thereby promoting the well−being of anammox bacteria. However, the excessive dosage of sulfide (S/N=1.8) intensified the DNRA process (contribution>35%) and weakened the anammox process, leading to an increase in effluent NH4+-N concentration and a decline in NRE. This study confirms that the in−situ adding an appropriate amount of sulfide favors achieving complete nitrogen removal in anammox system, which provides a novel avenue to resolve the issue of the residual nitrate in anammox process.

Lacticaseibacillus rhamnosus LRa05 alleviates cyclophosphamide-induced immunosuppression and intestinal microbiota disorder in mice.

Probiotics play a crucial role in regulating the gut microbiota and enhancing immune response. Oral administration of probiotics modulates intestinal microbiota composition and immune homeostasis. In this study, we investigated the immunoregulatory effect of Lacticaseibacillus rhamnosus LRa05 on cyclophosphamide (CTX)-induced immunosuppressive mice. The results showed that oral administration of LRa05 reduced weight loss, restored immune organ indices, and maintained the structural integrity of the intestinal tissue in CTX-treated mice. Moreover, oral administration of LRa05 exhibited immune-modulating properties by promoting the secretion of cytokines (tumor necrosis factor-α, interleukin-1β, interleukin-10, and secretory immunoglobulin A) in serum. Moreover, the analysis of 16S rRNA amplicon sequencing revealed that LRa05 increased gut microbiota diversity and regulated its composition. In detail, LRa05 intervention restored the Firmicutes/Bacteroidota ratio and significantly increased the relative abundance of Lachnospiraceae_NK4A136_group, Oscillibacter, Alloprevotella, Parasutterella, and Roseburia in immunocompromised mice. Conversely, the abundances of Helicobacter, Bacteroides, and unclassified_Desulfovibrionaceae were significantly decreased after administration of LRa05. Based on these findings, orally administered LRa05 could effectively maintain intestinal microbiota homeostasis and regulate immunity, suggesting the potential of L. rhamnosus LRa05 as a candidate probiotic strain in the application of dietary supplement. PRACTICAL APPLICATION: Supplement with L. rhamnosus LRa05 can improve immunity, regulate gut microbiota and promote body health.

Göttingen Minipigs as a Model for Assessing the Impact of Drugs on the Gut and Milk Microbiota—A Preliminary Study

Background: Early gut microbiota (GM) dysbiosis can affect a child’s health and has been linked to the onset of pathologies later in life. Breast milk is recognized as a major driver of the structure and dynamics of an infant’s GM. In addition to nutritious and prebiotic compounds, milk contains a microbiota that is shaped by several maternal factors, including gut microorganisms and medications. However, the impact of the latter on the milk microbiota is still largely unknown. Here, we investigated the effects of amoxicillin on the milk microbiota and GM of lactating Göttingen Minipigs sows, a promising model for studying medication transfer during lactation. Methods: Three sows were given amoxicillin (7 mg/kg/day) for three weeks starting from the second week after farrowing. Fecal and milk samples were collected before and after treatment and profiled by 16S rRNA amplicon sequencing. Results: Göttingen Minipigs’ milk microbiota showed similarities to that of humans and conventional sows, with minor compositional shifts after treatment. At the genus level, we observed a decrease in Staphylococcus and o_Bacteroidales;Other;Other, and an increasing trend in the abundance of Streptococcus, Stenotrophomonas, f_Rhodobacteraceae;Other, Proteiniclasticum, f_Propionibacteriaceae;Other and Gemella. In contrast, as expected, the GM was strongly affected by amoxicillin, even at the phylum level. Conclusions: In addition to demonstrating the relevance of Göttingen Minipigs as a valid model for studying the impact of medications on maternal milk and GM, our findings suggest that the milk microbiota may be more stable during antibiotic treatment than the GM.

PAH contamination in coastal surface sediments and associated bacterial communities

Polycyclic aromatic hydrocarbons (PAH) are semi-volatile, lipophilic, and harmful compounds that can persist for decades in a range of marine environments. There are several marine and soil microorganisms that possess enzymes involved in arene degradation. Here, we analyzed the structure (16S rRNA amplicons) and metabolic potential (inferred using phylogenetic placement) of the bacterial community in surface marine sediments from coastal waters off Concepción, Chile, and describe how microbial community patterns are shaped and altered by PAH contamination. Two depositional zones were identified, a “High PAH” area containing a mix of high and low molecular weight PAH of up to 10,350 ng∑PAH gdw−1 and with high organic matter content; and a “Low PAH” zone mostly characterized by low molecular weight PAH of up to 1810 ng∑PAH gdw−1 and lower levels of organic matter. We identified 53 hydrocarbonoclastic bacteria genera, with eight showing relatively high abundances at High PAH sites, although known PAH degrader clades were also present at Low PAH sites. With potential enzymes inferred in almost all samples, we suggest that breakdown of PAH is widespread in this area, likely resulting from the long history of local PAH emissions that may have promoted a stored microbial capacity for these degradation processes.

Monitoring Fish Bacterial Pathogens of Wild Fish Species From the South China Sea by Applying Next-Generation Sequencing on Gill Tissue.

The classic epidemiological triangle model of host-environment-pathogen is recently being reshaped into a tetrahedron, with the growing understanding of the importance of the microbiome in this array. The gills, being a gateway into the fish body, bearing an important role in fish homeostasis, host a complex microbiome that reflects the ambient water, while also showing resemblance to gut microbiome. Next-generation sequencing (NGS) and improvements in data analysis tools enable researchers to gather and analyse a lot more data than ever before, take a closer, more detailed look at microbiota, and gain a much better understanding of the biological processes at work in these complex relations. Here, 16S rRNA amplicons of bacterial DNA extracted from the gills of 36 asymptomatic specimens of three wild fish species from the South China Sea (Nemipterus japonicus, Alepes djebaba, and Saurida tumbil) were sequenced using NGS. Data analyses revealed the presence of 20 potentially pathogenic species, including several zoonotic agents. Gill microbiota exhibited host species-specificity, and expressed a significant difference between demersal and pelagic-amphidromous fish. It is suggested that this method be more widely implemented, in order to gain more insight on ocean ecosystems' health status, as well as fish stocks of commercial importance.

High-fat diet stimulated butyric acid metabolism dysbiosis, altered microbiota, and aggravated inflammatory response in collagen-induced arthritis rats.

Research has demonstrated that obesity may be associated with rheumatoid arthritis (RA). In addition, Dysbiosis of intestinal microbiota and their metabolites has been linked to the occurrence and development of RA and obesity. However, the mechanism by which obesity affects RA remains unclear.In this study, we explored the impact of high fat diet(HFD) on collagen-induced arthritis (CIA) rats and revealed its mechanisms based on gut microbiota and metabolomics. Based on diet and modeling, rats were divided into normal group (Con), CIA model group, HFD group (HFD), and HFD + CIA group (HCIA). The effect of HFD on arthritis in CIA rats were investigated based on the arthritis index (AI), weight, blood lipid levels, and inflammatory cytokines. Moreover, HE staining and micro-CT were performed to evaluated the effect of HFD on the pathology of joints and synovial tissues in CIA rats.16S rRNA amplicon sequencing and liquid chromatography-mass spectrometry (LC-MS) were employed to explore changes in gut microbiota and short-chain fatty acids (SCFAs). The AI scores, inflammatory cytokines and bone destruction parameters in the HCIA group were significantly higher than those in the other three groups. The results of 16S rRNA amplicon sequencing and metabolomics showed that compared with the other three groups, the expression of g_Muribaculaceae and butyric acid were reduced in the HCIA group. Spearman and linear correlation analyses revealed a positive correlation between g_Muribaculaceae abundance and butyric acid levels. HFD stimulated butyric acid metabolism dysbiosis, altered microbiota, and aggravated inflammatory response in CIA rats.

Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays

Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed.Key points• The applied methodology was successful to obtain biomass suitable to perform BMP assays.• The microbial community was resilient to external biomass addition.• Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.Graphical

Comparison of commonly used software pipelines for analyzing fungal metabarcoding data

BackgroundMetabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed and quality-filtered with bioinformatic pipelines. However, such pipelines are not yet standardized, especially for fungal communities, and those available may produce contrasting results. While some pipelines cluster sequences based on a specified percentage of base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques to infer amplicon sequencing variants (ASVs). While ASVs are now considered a more accurate representation of taxonomic diversity for prokaryote communities based on 16S rRNA amplicon sequencing, the applicability of this method for fungal ITS sequences is still debated.ResultsHere we compared the performance of two commonly used pipelines DADA2 (inferring ASVs) and mothur (clustering OTUs) on fungal metabarcoding sequences originating from two different environmental sample types (fresh bovine feces and pasture soil). At a 99% OTU similarity threshold, mothur consistently identified a higher fungal richness compared to DADA2. In addition, mothur generated homogenous relative abundances across multiple technical replicates (n = 18), while DADA2 results for the same replicates were highly heterogeneous.ConclusionsOur study highlights a potential pipeline-associated bias in fungal metabarcoding data analysis of environmental samples. Based on the homogeneity of relative abundances across replicates and the capacity to detect OTUs/ASVs, we suggest using OTU clustering with a similarity of 97% as the most appropriate option for processing fungal metabarcoding data.

Aerobic bacterial group as an early-stage biomarker from faecal samples of patients with colorectal cancer without distant metastasis.

The current approaches for detecting most colorectal polyps and early neoplasms lack sufficient sensitivity and specificity, potentially hindering treatment and ultimately reducing survival rates. Here, we performed a metagenomic analysis to identify microbiome markers in stool samples from patients with early-stage colorectal cancer (CRC). We compared the composition of gut microbiota between patients with CRC and healthy individuals, specifically focusing on patients with early-stage CRC, defined as those without core mutations (KRAS, BRAF) for CRC diagnosis, stable microsatellite instability, and distant metastasis. The aim of our study is to identify potential biomarkers from gut microbiota at different cancer stages in colorectal cancer (CRC) patients through 16S rRNA amplicon sequencing, thereby proposing a novel non-invasive method for the early diagnosis of CRC. Specific microbes were detected from groups divided based on the TNM criteria, with one group classified by tumour size only (named the T group) and another group with lymph node metastasis (named the TN group). Aerobic bacteria, such as Delftia, Stenotrophomonas, Sphingobacterium, Rhodococcus, Devosia, Ensifer, and Psychrobacter were predominantly detected in patients with CRC without lymph node metastasis. The diagnostic prediction was evaluated using the CatBoost algorithm; these microbes presented high diagnostic accuracy with a receiver operating characteristics-area under curve of 0.8, which was validated using qPCR. In conclusion, this study identified specific aerobic microbial groups as non-invasive biomarkers for early diagnosis in patients with CRC without genetic or environmental factors.

Stability in fecal metabolites amid a diverse gut microbiome composition: a one-month longitudinal study of variability in healthy individuals

ABSTRACT An extensive network of microbial-host interactions exists in the gut, making the gut microbiome a complex ecosystem to untangle. The microbial composition and the fecal metabolites are important readouts to investigate intricate microbiota-diet-host interplay. However, this ecosystem is dynamic, and it is of interest to understand the degree and timescale of changes occurring in the gut microbiota, during disease as well as in healthy individuals. Cross-sectional study design is often used to investigate the microbiome, but this design provides a static snapshot and cannot provide evidence on the dynamic nature of the gut microbiome. Longitudinal studies are better suited to extrapolate causation in a study or assess changes over time. This study investigates longitudinal change in the gut microbiome and fecal metabolites in 14 healthy individuals with weekly sampling over a period of one-month (four time points), to elucidate the temporal changes occurring in the gut microbiome composition and fecal metabolites. Utilizing 16S rRNA amplicon sequencing for microbiome analysis and NMR spectroscopy for fecal metabolite characterization, we assessed the stability of these two types of measurable parameters in fecal samples during the period of one month. Our results show that the gut microbiome display large variations between healthy individuals, but relatively lower within-individual variations, which makes it possible to uniquely identify individuals. The fecal metabolites showed higher stability over time compared to the microbiome and exhibited consistently smaller variations both within and between individuals. This relative higher stability of the fecal metabolites suggests a balanced, consistent output even amid individual’s differences in microbial composition and they can provide a viable complementary readout to better understand the microbiome activity.

Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries.

The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.

Investigating the Effects of Elevation on Microbial Communities and Soil Properties at Fanjing Mountain, China

Elevation is one of the most influential factors affecting soil characteristics and microbial communities in forest ecosystems. Nevertheless, there is no consensus on how soil characteristics, soil microbials, and their relationships response to the elevation of the mountain ecosystem. We investigated the soil physicochemical characteristics, the activity of soil enzymes, and the microbial community at elevational sites from 600 to 2400 m above sea level (asl) in the western slopes of the Fanjing Mountain ecosystem, China. The soil microbial communities were determined by high throughput 16S rRNA and ITS amplicon sequencing. The results demonstrated that soil total nitrogen (TN) showed a slight decrease, whereas total phosphorus (TP) and total potassium (TK) gradually tended to increase with increasing elevation. The large macroaggregates (>2 mm) accounted for the largest proportion of the aggregate fraction (66.23%–76.13%) in the 0–10 cm soil layer with elevation. The average values of the soil electrical conductivity (EC), soil organic carbon (SOC), and cation exchange capacity (CEC) concentration in the 0–60 cm layer undulated with increasing elevation, and the highest values were observed at 1500–1800 m asl and 1800–2100 m asl, respectively. The activities of soil urease, sucrase, acid phosphatase, and catalase clearly differed (p < 0.05) with increasing elevation, and the minimum values were found at 2100–2400 m asl. Interesting, with increasing soil depth, the values of these factors tended to decrease, indicating surface aggregation. In addition, the soil microbial (bacterial and fungal) community diversity exhibited a single-peak pattern with elevation. Our results also revealed that the soil bacterial and fungal communities varied significantly at different elevation sites. The bacterial communities were dominated by the phyla Acidobacteria, Pseudomonadota, and Chloroflexi, and the phyla Basidiomycota and Ascomycota dominated the fungal communities. The Pearson and redundancy analyses revealed that the SOC, TP, four soil enzymes, and soil aggregates were significant factors influencing the soil microbial community. In conclusion, soil properties and enzyme activities jointly explained the elevational pattern of the soil microbial community in the Fanjing Mountain. The results of this study provide insights into the influence of elevation on soil characteristics, microbial communities, and their relationships in the Fanjing Mountain ecosystem.

Benefits of Crotalaria juncea L. as Green Manure in Fertility and Soil Microorganisms on the Peruvian Coast.

The soils of the Barranca valley are among the best soils in Peru, but with so many years of application of agrochemicals and other agricultural practices, they are losing their productive capacity. Consequently, it was suggested to assess the impact of Crotalaria juncea L. as a green manure on soil fertility and the populations of bacteria and fungi present in the soil. Crotalaria was cultivated for 75 days and incorporated as green manure. After 90 days, the presence of bacteria and fungi was evaluated. Metabarcoding was employed, and the 16S rRNA and ITS2 amplicons were sequenced using the Illumina MiSeq platform. The sequences were processed using various bioinformatics tools. The results indicate that soils have a high diversity of bacteria and fungi. Likewise, in plots where the presence and action of natural biocontrol is suppressed (C0 and P0), pathogenic fungi increase their population in the fallow period (C1), while in P1, the addition of Crotalaria as a green manure promotes an increase in the population of bacteria and fungi, and at the same time it suppresses pathogenic fungi. The genera (bacterial and/or fungal) that increase due to the effect of Crotalaria are beneficial because they are involved as degraders of organic matter, promotion of plant growth and biological control of pathogens. Crotalaria is an alternative to improve soil fertility, increase the beneficial bacterial population, and reduce pathogenic fungi.

Endophytic Bacillus velezensis GsB01 controls Gleditsia sinensis wilt by secreting antifungal metabolites and modulates symbiotic microbiota within trees.

Identifying effective biological control agents against fungal pathogens and determining their mechanisms of action are important in the control of plant diseases. In this study, we isolated an endophytic bacterial strain, GsB01, from the branches of asymptomatic Gleditsia sinensis. Multi-locus sequence analysis identified the strain as Bacillus velezensis. GsB01 exhibited significant antifungal activity against Thyronectria austroamericana, the causative agent of G. sinensis wilt. Liquid chromatography-mass spectrometry identified four consistently present antimicrobial compounds in GsB01 metabolite fractions with high antifungal activity: macrolactin A, bacillaene A, surfactin, and iturin. GsB01's active metabolite fractions altered the metabolic profiles of T. austroamericana, disrupting seven pathways, including arginine biosynthesis, nucleotide metabolism, purine metabolism, and the pentose phosphate pathway. Furthermore, absolute quantitative polymerase chain reaction analysis suggested that GsB01 may increase the abundance of endophytic bacteria in G. sinensis. The 16S rRNA amplicon sequencing revealed changes in the endophytic landscape in stems and roots following GsB01 introduction, particularly with significant variation in the dominant bacterial genera within the stems. The study highlights GsB01's potential against plant wilt and suggests that its antifungal activity is achieved by secreting antifungal metabolites. The study also recorded changes in the symbiotic microbiota within trees that had been infected with a pathogenic fungus and subsequently treated with an endophytic antagonistic bacterial strain. © 2024 Society of Chemical Industry.

Wastewater-associated plastispheres: A hidden habitat for microbial pathogens?

Wastewater treatment plants (WWTPs) receive wastewater from various sources. Despite wastewater treatment aiming to remove contaminants, microplastics persist. Plastic surfaces are quickly colonized by microbial biofilm ("plastispheres"). Plastisphere communities are suggested to promote the spread and survival of potential human pathogens, suggesting that the transfer of plastispheres from wastewater to the environment could pose a risk to human and environmental health. The study aimed to identify pathogens in wastewater plastispheres, specifically food-borne pathogens, in addition to characterizing the taxonomic diversity and composition of the wastewater plastispheres. Plastispheres that accumulated on polypropylene (PP), polyvinyl chloride (PVC), and high-density polyethylene propylene (HDPE) surfaces exposed to raw and treated wastewater were analyzed via cultivation methods, quantitative reverse transcription PCR (RT‒qPCR) and 16S rRNA amplicon sequencing. RT‒qPCR revealed the presence of potential foodborne pathogenic bacteria and viruses, such as Listeria monocytogenes, Escherichia coli, norovirus, and adenovirus. Viable isolates of the emerging pathogenic species Klebsiella pneumoniae and Acinetobacter spp. were identified in the plastispheres from raw and treated wastewater, indicating that potential pathogenic bacteria might survive in the plastispheres during the wastewater treatment. These findings underscore the potential of plastispheres to harbor and disseminate pathogenic species, posing challenges to water reuse initiatives. The taxonomic diversity and composition of the plastispheres, as explored through 16S rRNA amplicon sequencing, were significantly influenced by the wastewater environment and the duration of time the plastic spent in the wastewater. In contrast, the specific plastic material did not influence the bacterial composition, while the bacterial diversity was affected. Without efficient wastewater treatment and proper plastic waste management, wastewater could act as a source of transferring plastic-associated pathogens into the food chain and possibly pose a threat to human health. Continued research and innovation are essential to improve the removal of microplastics and associated pathogenic microorganisms in wastewater.

Lactobacillus rhamnosus modulates murine neonatal gut microbiota and inflammation caused by pathogenic Escherichia coli

BackgroundPathogenic Escherichia coli strains produce neonatal septicemia after colonizing the neonatal gut. While the probiotic Lactobacillus rhamnosus GG (LGG) effectively reduces neonatal sepsis, LGG’s effects on the neonatal intestinal microbiota alterations and inflammation triggered by E. coli are incompletely understood. We hypothesized that LGG significantly modulates the specific neonatal gut microbial populations changes and the inflammatory response elicited by the enteral introduction of septicemia-producing E. coli. To test this hypothesis, newborn rats were pretreated orally with LGG or placebo prior to infection with the neonatal E. coli septicemia clinical isolate SCB34. Amplicon 16S rRNA gene sequencing was performed on intestinal samples. Intestinal injury and expression of inflammatory mediators and apoptosis were determined.ResultsAlpha diversity of gut microbiota was greater in SCB34-infected pups in comparison to sham-infected pups, these changes were not modified by LGG pretreatment. Beta diversity analyses also showed differences between SCB34-infected vs. uninfected pups. LGG pretreatment before SCB34 infection did not result in significant beta diversity changes compared to placebo. Moreover, individual genera and species abundance analyses by linear discriminant analysis effect size (LEfSe) showed significant changes in Gram-negative, Gram-positive, and anaerobic populations resulting from LGG pretreatment and SCB34 infection. LGG significantly suppressed the expression of inflammatory cytokines but did not attenuate SCB34-induced apoptosis or histologic injury.ConclusionsLGG modulates clinically significant microbiota features and inflammation triggered by pathogenic E. coli intestinal infection shortly after birth. This new knowledge can potentially be harnessed to design novel interventions against gut-derived neonatal sepsis.

Fecal and Sputum Microbiota and Treatment Response in Patients with Mycobacterium abscessus Pulmonary Disease.

The microbiota is a potential source of biomarkers for clinical outcomes in chronic respiratory conditions, but its role in Mycobacterium abscessus pulmonary disease (PD) remains unexplored. We aimed to identify microbial signatures in fecal and sputum microbiotas associated with treatment response in patients with M. abscessus PD. We conducted a cohort study prospectively enrolling patients undergoing antibiotic treatment for M. abscessus PD. Fecal and sputum samples were collected before, and 2 weeks and 6 months after, treatment initiation. 16S rRNA amplicon sequencing approach was used to characterize the microbiotas. After categorizing patients as early treatment responders and non-responders based on sputum culture results at 2 weeks, we elucidated the differences in their diversity and composition of microbiotas. Among 32 patients enrolled, 27 patients (median 66 years, 85.2% women, 48.1% with subspecies abscessus) were included for microbiota analysis. Fifteen patients (55.6%) achieved negative conversion at 2 weeks, which was maintained in 14 (93.3%) after 6 months. Alpha-diversity of the fecal microbiota after 2 weeks of treatment decreased significantly in responders, but not in non-responders (P=0.029). Increased abundance of Eubacterium hallii group in baseline fecal microbiota was indicative of unresponsiveness to antibiotics, whereas an increase in Enterococcus in fecal microbiota at week 2 was linked with favorable response. Increased abundance of Burkholderia-Caballeronia-Paraburkholderia and Porphyromonas in baseline, and decreased abundance of Rothia in week 2 sputum microbiota were also associated with good treatment response. In M. abscessus PD, changes in microbial diversity and compositional signatures vary with treatment response.

Study on the Structure and Function of Intestinal Microorganisms in Silkworm Maggot Exorista sorbillans

ABSTRACTInsects have important symbiotic relationships with their intestinal microbiota. The intestinal microbiota is involved in or influences various processes in insects such as development, metabolism, immunity, and reproduction. Currently, research on the intestinal microbiota of parasitic insects is still in its early stages. The tachinid parasitoid Exorista sorbillans is a dipteran parasitic insect, with the silkworm (Bombyx mori) being its main host. Silkworms parasitized by E. sorbillans can suffer from severe silkworm maggot disease, which also poses a serious threat to sericulture. In this study, the intestinal microbiota of larval E. sorbillans at three instar stages was analyzed using 16S rRNA amplicon sequencing to explore the community composition of the intestinal microbiota. Additionally, using conventional culture methods, six cultivable strains were isolated and identified from the larval E. sorbillans on an antibiotic‐free LB medium, and four cultivable strains were isolated and identified from the hemolymph of parasitized silkworms. This study investigated the E. sorbillans from the perspective of intestinal microbiota, elucidating the composition and structural characteristics of the intestinal microbiota of the tachinid parasitoid, and preliminarily discussing the functional roles of several major microorganisms, which helps to further clarify the potential mechanisms of interaction between the parasitoid and the silkworm.

SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas

Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.