Related Microbes Research Articles

Nutraceuticals and pharmacological to balance the transitional microbiome to extend immunity during COVID-19 and other viral infections

Abstract Scope The underlying medical conditions and gut dysbiosis is known to influence COVID-19 severity in high-risk patients. The current review proposed the optimal usage of nutraceuticals & pharmacological interventions can help regulate the protective immune response and balance the regulatory functionality of gut microbiota. Summary Many studies have revealed that the probiotic interventions viz., Lactobacillus rhamnosus, L. plantarum & other bacterial spp. reduce IFNγ & TNF-α and increase IL-4 & IL-10 secretions to control the immunostimulatory effects in upper respiratory tract infection. Dietary fibres utilized by beneficial microbiota and microbial metabolites can control the NF-kB regulation. Vitamin C halts the propagation of pathogens and vitamin D and A modulate the GM. Selenium and Flavonoids also control the redox regulations. Interferon therapy can antagonize the viral replications, while corticosteroids may reduce the death rates. BCG vaccine reprograms the monocytes to build trained immunity. Bifidobacterium and related microbes were found to increase the vaccine efficacy. Vaccines against COVID-19 and season flu also boost the immunity profile for robust protection. Over all, the collective effects of these therapeutics could help increase the opportunities for faster recovery from infectious diseases. Conclusion The nutraceutical supplements and pharmacological medicines mediate the modulatory functionalities among beneficial microbes of gut, which in turn eliminate pathogens, harmonize the activity of immune cells to secrete essential regulatory molecular receptors and adaptor proteins establishing the homeostasis in the body organs through essential microbiome. Therefore, the implementation of this methodology could control the severity events during clinical sickness and reduce the mortalities.

Comparative Antimicrobial Efficacy of Garlic and Guava Extracts on Oral Pathogens Using a Time Kill Assay: An In Vitro Study

Abstract Background: Periodontal disease is characterized by inflammation mediated by the host and related microbes, which leads to the loss of periodontal attachment and tooth loss. Due to an increase in bacterial resistance to antibiotics, there is a shift toward use of herbal medicines. Aim: The aim of the study is to compare the antimicrobial effect of aqueous garlic extract (AGE) and ethanolic guava extract (EGuE) on Tanerella forsythia and Porphyromonas gingivalis using the time kill assay Materials and Methods: AGE and EGuE are prepared. Ciprofloxacin was taken as the control. The MIC was performed for garlic, guava extract, and ciprofloxacin. P. gingivalis and T. forsythia were cultured, and the time kill assay was performed at 0 h, 5 min, 30 min, 1 h, and 2 h. Colonies were counted after 48–72 h for growth. Results: The minimal inhibitory concentration (MIC) results indicated that both EGuE and AGE exhibited superior antibacterial activity compared to ciprofloxacin, suggesting their potential as alternative or complementary antimicrobial agents. In a time kill assay, EGuE demonstrated a significant reduction in colony forming units (CFUs) at 30 min, 1 h, and 2 h, outperforming AGE and ciprofloxacin. Intragroup comparisons revealed that EGuE significantly reduced CFUs at 0 h and 5 min, while AGE showed no notable reduction over time. Conclusion: Overall, the study demonstrates the antimicrobial efficacy of EGuE and AGE against T. forsythia and P. gingivalis at higher concentrations. Hence, these extracts may serve as alternative antimicrobial agents against periodontal pathogens.

Effect of plant development on phosphorus fractions and microbial phosphorus cycle in subsurface flow constructed wetlands

Plant development can influence the effluent concentrations of total phosphorus (TP) in constructed wetlands (CWs). However, little is known regarding the effect of plant development on P cycling in CWs. In this study, Juncus effusus was selected as wetland plant. The P removal efficiency, the change of P fractions in substrate and the relative abundance of P cycling genes were investigated along with plant development in CWs over seedling, mature, and wilting stages. The results showed that the effluent concentration of TP in CWs varied towards higher levels along with the plant development, and significant differences from the previous two stages were observed at the wilting stage. P fractions in the substrate accumulated with continuing influent, providing conditions for P cycling. There were differences in the relative abundance of functional genes involved in P cycling at different stages of plant development. With plant development, microbial transportation of P (indicated by the genes of phnCDE and ugpABCE) was weakened and then enhanced, while in contrast inorganic P solubilization (indicated by the genes of gcd) and organic P mineralization (indicated by the genes of phnP and phnW) were enhanced and then weakened. Pearson correlation analysis results indicated that the P cycling in the substrate of CWs was enriched with plant development, which promoted labile P accumulation in the CW substrate, resulting in higher effluent TP concentration at the wilting stage. Plant development was found to influence P cycling related microbes by regulating the relative abundance of genes involved in P cycling. The acquired results provided new insights into the effect of plant development on P cycling and effluent TP concentration stabilization in CWs.

Deciphering the roles of nitrogen source in sharping synchronous metabolic pathways of linear alkylbenzene sulfonate and nitrogen in a membrane biofilm for treating greywater

Nitrogen (N) source is an important factor affecting biological wastewater treatment. Although the oxygen-based membrane biofilm showed excellent greywater treatment performance, how N source impacts the synchronous removal of organics and N is still unclear. In this work, how N species (urea, nitrate and ammonia) affect synchronous metabolic pathways of organics and N were evaluated during greywater treatment in the membrane biofilm. Urea and ammonia achieved efficient chemical oxygen demand (>97.5%) and linear alkylbenzene sulfonate (LAS, >98.5%) removal, but nitrate enabled the maximum total N removal (80.8 ± 2.6%). The nitrate-added system had poor LAS removal ratio and high residual LAS, promoting the accumulation of effluent protein-like organics and fulvic acid matter. N source significantly induced bacterial community succession, and the increasing of corresponded functional flora can promote the transformation and utilization of microbial-mediated N. The nitrate system was more conducive to the accumulation of denitrification related microorganisms and enzymes, enabling the efficient N removal. Combining with high amount of ammonia monooxygenase that contributing to LAS and N co-metabolism, LAS mineralization related microbes and functional enzymes were generously accumulated in the urea and ammonia systems, which achieved the high efficiency of organics and LAS removal.

PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification.

Profiling microbial communities at high resolution and with absolute quantification is essential to uncover hidden ecological interactions within microbial ecosystems. Nevertheless, achieving resolved and quantitative investigations has been elusive due to methodological limitations in distinguishing and quantifying highly related microbes. Here, we describe Phylogenetically Unique Primers in python (PUPpy), an automated computational pipeline to design taxon-specific primers within defined microbial communities. Taxon-specific primers can be used to selectively detect and quantify individual microbes and larger taxa within a microbial community. PUPpy achieves substrain-level specificity without the need for computationally intensive databases and prioritizes user-friendliness by enabling both terminal and graphical user interface applications. Altogether, PUPpy enables fast, inexpensive, and highly accurate perspectives into microbial ecosystems, supporting the characterization of bacterial communities in both in vitro and complex microbiota settings.

Nitrogen release and microbial community characteristics during the decomposition of field‐incorporated corn straw in Northeast China

AbstractStraw incorporation increases the amount of nutrients in soil and greatly impacts soil nitrogen and microbial communities. In this study, 15N‐labeled corn straw was used as the material, the experiment consisted of five treament (AS: placing the straw 15 cm above the soil surface, SM: using the straw to mulch the soil surface, B15: burying the straw 15 cm below the ground surface, B30: burying the straw 30 cm below the ground surface, B45: burying the straw 45 cm below the ground surface). The changes in 15N abundance in straw were analyzed. An estimation method for nitrogen release and uptake by field‐incorporated straw was proposed, and the relationships between nitrogen release and uptake and related microbes were established. The results showed that the exchange of nitrogen between maize straw buried in soil at different depths and the environment was not significant. The corn straw exposed to the air absorbed more nitrogen from the environment in the second year of decomposition, and the larger the area exposed to the air was, the more nitrogen was absorbed from the environment. The relative abundances of Burkholderiales, Flavobacteriales, Pseudomonadales, and Sphingobacteriales were significantly positively correlated with the straw decomposition rate and nitrogen release rate. The relative abundance of Rhizobiales was significantly negatively correlated with the straw decomposition rate and nitrogen release rate. The relative abundances of Sphingobacteriales, Flavobacteriales, and Pseudomonadales were significantly negatively correlated with the straw nitrogen uptake rate.

Detection and Antimicrobial Susceptibility of Candida Species Isolated from the Urine of Patients in a Tertiary Health Facility, Southwest Nigeria

Aims: This study aimed to identify and determine the antimicrobial susceptibility profiles of Candida species causing UTI among patients attending a tertiary Teaching Hospital, in southwest Nigeria. Study Design: Comparative cross-sectional study. Place and Duration of Study: Lagos State University Teaching Hospital, Ikeja, Nigeria between June 2017 and February, 2018. Methodology: A total of 250 participants whose provisional diagnosis was candiduria were recruited for this study. Urine samples were collected from consenting participants early in the morning into sterile wide mouth universal containers. These samples were cultured aerobically on Blood agar, Cystine-Lactose-Electrolyte Deficient (CLED) agar and Sabouraud dextrose agar (SAB) at 370C within 1 to 2 days. The isolates were profiled into species level using microscopic, biochemical test, chromogenic media (Chrom agar Candida) and Analytical Profile Index (API) 32C examination analysis. Results: An overall rate for Candidiasis in this study was 12.8% (32/250). The rate was higher in female 17.5% compared to 6.5% in their male counterparts (p=0.014). Highest rate of infections peaked at 28.6% among age group 83-92 years and lowest (6.7%) in age group 23-32 years. A total of 11 (4.4%) urine culture from participants produced C. albicans pure fungi isolates. However, by gender, this was statistically significant (p=0.003). A total of 81 bacterial (32.4%) and fungal isolates 32 (12.8%) were isolated and profiled. Distribution of Candida species indicated highest incidence in age range 31-40 years, followed by 21-30years and age 61-70 years age brackets. The isolated species were Candida albicans 11(34.4%), C. tropicalis 8(25%), C. parapsilopsis 6(19%), C. krusei 2(6.3%) and C. hellenica 1(3.1%). Sixty to seventy percent of fungal isolates were susceptible to ketoconazole and fluconazole while the susceptibility pattern of Candida species to itraconazole, terbinafine and nystatin varied between moderately susceptible to resistance. All the Candida isolates were resistant to griseofulvin. However, C. albicans was found to be the major Candida species causing Candidal urinary tract infection. The only C. hellenica isolated was resistant to all the antifungal drugs were approved except nystatin. Conclusion: High profile of Candida isolates and related UTI microbes were found in this study. There is need for advocacy for the use of API and Chrom agar Candida for routine diagnosis for Candida identification. Nevertheless, the Candida isolates were mostly susceptible to ketoconazole and Fluconazole but only the isolates were griseofulvin resistant.

Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer

BackgroundColorectal cancer (CRC) is the leading cancer worldwide. Microbial agents have been considered to contribute to the pathogenesis of different disease. But the underlying relevance between CRC and microbiota remain unclear.MethodsWe dissected the fecal microbiome structure and genomic and transcriptomic profiles of matched tumor and normal mucosa tissues from 41 CRC patients. Of which, the relationship between CRC-associated bacterial taxa and their significantly correlated somatic mutated gene was investigated by exome sequencing technology. Differentially expressed functional genes in CRC were clustered according to their correlation with differentially abundant species, following by annotation with DAVID. The composition of immune and stromal cell types was identified by XCELL.ResultsWe identified a set of 22 microbial gut species associated with CRC and estimate the relative abundance of KEGG ontology categories. Next, the interactions between CRC-related gut microbes and clinical phenotypes were evaluated. 4 significantly mutated gene: TP53, APC, KRAS, SMAD4 were pointed out and the associations with cancer related microbes were identified. Among them, Fusobacterium nucleatum positively corelated with different host metabolic pathways. Finally, we revealed that Fusobacterium nucleatum modified the tumor immune environment by TNFSF9 gene expression.ConclusionCollectively, our multi-omics data could help identify novel biomarkers to inform clinical decision-making in the detection and diagnosis of CRC.

A study on the association between gut microbiota, inflammation, and type 2 diabetes

Type 2 diabetes mellitus (T2DM) was reported to be associated with impaired immune response and alterations in microbial composition and function. However, the underlying mechanism remains elusive. To investigate the association among retinoic acid-inducible gene-I-like receptors (RLRs) signaling pathway, intestinal bacterial microbiome, microbial tryptophan metabolites, inflammation, and a longer course of T2DM, 14 patients with T2DM and 7 healthy controls were enrolled. 16S rRNA amplicon sequencing and untargeted metabolomics were utilized to analyze the stool samples. RNA sequencing (RNA-seq) was carried out on the peripheral blood samples. Additionally, C57BL/6J specific pathogen-free (SPF) mice were used. It was found that the longer course of T2DM could lead to a decrease in the abundance of probiotics in the intestinal microbiome. In addition, the production of microbial tryptophan derivative skatole declined as a consequence of the reduced abundance of related intestinal microbes. Furthermore, low abundances of probiotics, such as Bacteroides and Faecalibacterium, could trigger the inflammatory response by activating the RLRs signaling pathway. The increased level of the member of TNF receptor-associated factors (TRAF) family, nuclear factor kappa-B (NF-κB) activator (TANK), in the animal colon activated nuclear factor kappa B subunit 2 (NFκB2), resulting in inflammatory damage. In summary, it was revealed that the low abundances of probiotics could activate the RLR signaling pathway, which could in turn activate its downstream signaling pathway, NF-κB, highlighting a relationship among gut microbes, inflammation, and a longer course of T2DM.Key pointsHyperglycemia may suppress tryptophanase activity.The low abundance of Bacteroides combined with the decrease of Dopa decarboxylase (DDC) activity may lead to the decrease of the production of tryptophan microbial derivative skatole, and the low abundance of Bacteroides or reduced skatole may further lead to the increase of blood glucose by downregulating the expression of glucagon-like peptide-1 (GLP1).A low abundance of anti-inflammatory bacteria may induce an inflammatory response by triggering the RLR signaling pathway and then activating its downstream NF-κB signaling pathway in prolonged T2DM.

Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO2 vents

Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3–V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.

Conceptual Study of Balgrahas (Microbes) in Kaumarbhritya: A Narrative Review

Ayurveda is a time-tested science that systematically explains its concepts through eight branches. Grahas Chikitsa (Ayurvedic treatment of microbes) is one of these branches, and it is well-explained in the texts. “Graha” refers to a tiny, invisible living organism that may undergo several stages of development and can be pathogenic or antigenic to the body. Microorganisms can cause generalised pathogenic alterations in the body that affect multiple systems, similar to the concept of Grahas. This suggests a deeper understanding of microbes in relation to Grahas. This review paper aims to explore the age-old concept of Balgrahas (microbes) and its relevance in modern times. The review was conducted using published articles on paediatric disorders, electronic databases, textbooks on paediatrics, and traditional Ayurvedic writings related to Kauamarbhritya (Paediatrics). A distinguishing feature of this study is its compilation of information on Balgraha from classical texts, covering clinical characteristics, causal factors, and various internal and external treatments. It also discusses Ayurvedic treatment modalities such as Daiva Vyapashraya Chikitsa (Spiritual therapy) and Yukti Vyapashraya Chikitsa (Rational therapy). In this review, authors discussed several formulations for treating conditions associated with Balgraha (microbes) that have not been detailed in previous studies. Additionally, some Shodhan karma (Detoxification) procedures that are particularly recommended for both children and nursing mothers are also highlighted.

Shatianyu (Citrus grandis L. Osbeck) whole fruit alleviated loperamide-induced constipation via enhancing gut microbiota-mediated intestinal serotonin secretion and mucosal barrier homeostasis.

This study aims to explore the effects of Shatianyu (Citrus grandis L. Osbeck) whole fruit powder (SWFP) enriched in flavonoids and dietary fiber on loperamide-induced constipation after a 4-week administration in the diet, together with possible microbiota-mediated mechanisms. The SWFP intervention shortened the first defecation time and increased defecation frequency; it also increased the serum serotonin (5-HT) level and decreased the LPS level in constipation mice. SWFP promoted the development of colonic enterochromaffin cells (ECs) and upregulated the expression of 5-HT synthetic rate-limiting enzyme (Tph1) in ECs. Furthermore, SWFP downregulated the expression of colonic TLR-4, TNF-α and IL-1β and upregulated the expression of tight junction proteins. Besides promoting 5-HT secretion in ECs, butyrate was proved to play a positive role in enhancing intestinal barrier homeostasis through FFAR2/3. Notably, SWFP increased both the fecal butyrate contents and colonic FFAR3 expression in a dose-related manner. Likewise, SWFP enriched butyrate-production related microbes, such as Ruminococcus_torques_group, Ruminococcus, Dubosiella and Parasutterella. Thus, SWFP might alleviate constipation by regulating the microbiota to produce butyrate, thereby enhancing colonic 5-HT secretion and the FFAR3-mediated anti-inflammatory pathway.

1426. Integrating artificial intelligence and dynamic programming to identify microbial clusters through antimicrobial susceptibility sequence analysis

Abstract Background The spread of infectious diseases and antimicrobial resistance poses a significant threat, especially in developing countries where traditional DNA fingerprinting techniques are often not available. We propose a novel approach using dynamic programming algorithms to compare antimicrobial susceptibility sequences and identify clusters of related microbes. Methods We selected pathogens from specific infections and tested them with a range of antimicrobials, recording the test results as either sensitive (S), resistant (R), or unknown (U) to each drug. These results were combined into a sequence, or ATB string, for each pathogen (Fig. 1). To compare the sequences, we used dynamic programming (Fig. 2) to calculate the minimum edit distance between each pair of sequences. The edit distance reflects the number of atomic changes needed to transform one sequence into the other. In this case, atomic changes include insertion, deletion, substitution, and matching of individual test results (Fig. 3). We created a matrix of pairwise similarities by comparing all ATB strings. A cluster of similar strains was identified based on a cutoff in the edit distance matrix, such as a distance of less than 1. The method, which is available in the SACIH+ system (https://plus.sacihweb.com), was used to analyze the same strain of specific healthcare infections from a public hospital in Belo Horizonte, Brazil, diagnosed between Jan 2022 and Mar 2023.Figure 1.Antimicrobial testing and ATB string generation for selected pathogens. Antimicrobial testing and ATB string generation for selected pathogens.Figure 2.Sequence comparison using dynamic programming. Sequence comparison using dynamic programming. Results We analyzed S. aureus strains from surgical site infection - SSI (23 cases), pneumonia - PNEU (29 cases), and bloodstream infection - BSI (13 cases). Identified 4 SSI, 10 PNEU clusters (Fig. 4 and 5), and 4 BSI clusters using edit distance matrix. For K. pneumoniae strains from 21 BSI, 22 PNEU, and 34 urinary tract infection - UTI cases, found 5 clusters for PNEU and UTI, and 7 clusters for BSI (Fig. 6).Figure 3.Minimum edit distance calculation for sequence comparison. Minimum edit distance calculation for sequence comparison.Figure 4.Clustering of Staphylococcus aureus strains from 29 nosocomial pneumonia cases. Clustering of Staphylococcus aureus strains from 29 nosocomial pneumonia cases.Figure 5.Identification of a large cluster with 16 identical Staphylococcus aureus strains from 29 nosocomial pneumonia cases.Identification of a large cluster with 16 identical Staphylococcus aureus strains from 29 nosocomial pneumonia cases. Conclusion Our novel approach using dynamic programming to compare antimicrobial susceptibility sequences has shown promise in identifying clusters of related microorganisms, even without traditional DNA fingerprinting methods. The method represents a valuable tool for tracking the spread of infectious diseases, especially in settings where traditional methods are not available.Figure 6.Clustering of Klebsiella pneumoniae strains from 21 bloodstream infection cases.Clustering of Klebsiella pneumoniae strains from 21 bloodstream infection cases. Disclosures All Authors: No reported disclosures

Microbial nitrogen mineralization is slightly affected by conversion from farmland to apple orchards in thick loess deposits

Organic nitrogen mineralization, indispensable to soil carbon and nitrogen cycles, is the largest contributor to nitrate reservoirs in deep vadose zones. The microbial nitrogen mineralization (MNM) within deep soils, particularly in regions with intensive agricultural activities and thick soil horizons, has been largely disregarded. As such, this study aims to address this knowledge gap by investigating the chiA-harboring microbial structure and network within nine 10-m profiles beneath cultivated farmland and two apple orchards. The results showed that apple orchards, compared to farmland, had considerable water deficit and nitrogen accumulation within deeper soil layers due to well-developed root systems and the overuse of chemical fertilizers. However, the chiA-harboring microbial diversity, composition, and abundance all exhibited significant variations with soil depths rather than being influenced by different land use types. Moreover, the diversity indices and gene abundances decreased with soil depths, and the related soil microbes included 19 phyla, 29 classes, 72 orders, 114 families, and 197 genera, with Actinobacteria and Proteobacteria being the two major bacterial phyla. The microbial co-occurrence network was simper beneath apple orchards. The chiA-harboring microorganisms within deep unsaturated zones were greatly influenced by the depth-dependent soil nutrients, such as total nitrogen, organic carbon, and available potassium. The limited plant root biomass and the inhibitory effects of dried soil layers both restricted the availability of carbon sources, which further interfered with the MNM processes within deep soils insignificantly. Therefore, despite the considerable plant-induced ecohydrological consequences, the depth-dependent MNM processes were slightly affected after the transformation from farmland to apple orchards within thick loess deposits. This study offers crucial insights into microbial dynamics of the deep biosphere, thereby contributing to our understanding of depth-dependent biogeochemical cycles within global deep unsaturated zones.

The Improvement of Fluorescence In Situ Hybridization Technique Based on Explorations of Symbionts in Cicadas.

Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is widely used for the identification of microbes in complex samples, but it suffers from some limitations resulting in the weak or even absence of fluorescence signals of microbe(s), which may lead to the underestimation or misunderstanding of a microbial community. Herein, we explored symbionts in the bacteriomes and fat bodies of cicadas using modified FISH, aiming to improve this technique. We initially revealed that the probes of Candidatus Sulcia muelleri (Sulcia) and the yeast-like fungal symbiont (YLS) are suitable for detection of these symbionts in all cicadas and some other species of Auchenorrhyncha, whereas the probe of Candidatus Hodgkinia cicadicola (Hodgkinia) is only suitable for detection of Hodgkinia in a few cicada species. The fluorescence signal of Sulcia, Hodgkinia and YLS exhibited weak intensity without the addition of unlabeled oligonucleotides (helpers) and heat shock in some cicadas; however, it can be significantly improved by the addition of both helpers and heat shock. Results of this study suggest that heat shock denaturing rRNA and proteins of related microbe(s) together with helpers binding to the adjacent region of the probe's target sites prevent the re-establishment of the native secondary structure of rRNA; therefore, suitable probe(s) can more easily access to the probe's target sites of rRNA. Our results provide new information for the significant improvement of hybridization signal intensities of microbes in the FISH experiment, making it possible to achieve a more precise understanding of the microbial distribution, community and density in complex samples.

Bacterial bioconvection confers context-dependent growth benefits and is robust under varying metabolic and genetic conditions.

Microbes often respond to environmental cues by adopting collective behaviors-like biofilms or swarming-that benefit the population. During "bioconvection," microbes gather in dense groups and plume downward through fluid environments, driving flow and mixing on the scale of millions of cells. Though bioconvection was observed a century ago, the effects of differing physical and chemical inputs and its potential selective advantages for different species of microbes remain largely unexplored. In Bacillus subtilis, vertical oxygen gradients that originate from air-liquid interfaces create cell-density inversions that drive bioconvection. Here, we develop Escherichia coli as a complementary model for the study of bioconvection. In the context of a still fluid, we found that motile and chemotactic genotypes of both E. coli and B. subtilis bioconvect and show increased growth compared to immotile or non-chemotactic genotypes, whereas in a well-mixed fluid, there is no growth advantage to motility or chemotaxis. We found that fluid depth, cell concentration, and carbon availability affect the emergence and timing of bioconvective patterns. Also, whereas B. subtilis requires oxygen gradients to bioconvect, E. coli deficient in aerotaxis (Δaer) or energy-taxis (Δtsr) still bioconvects, as do cultures that lack an air-liquid interface. Thus, in two distantly related microbes, bioconvection may confer context-dependent growth benefits, and E. coli bioconvection is robustly elicited by multiple types of chemotaxis. These results greatly expand the set of physical and metabolic conditions in which this striking collective behavior can be expected and demonstrate its potential to be a generic force for behavioral selection across ecological contexts. IMPORTANCE Individual microorganisms frequently move in response to gradients in their fluid environment, with corresponding metabolic benefits. At a population level, such movements can create density variations in a fluid that couple to gravity and drive large-scale convection and mixing called bioconvection. In this work, we provide evidence that this collective behavior confers a selective benefit on two distantly related species of bacteria. We develop new methods for quantifying this behavior and show that bioconvection in Escherichia coli is surprisingly robust to changes in cell concentration, fluid depth, interface conditions, metabolic sensing, and carbon availability. These results greatly expand the set of conditions known to elicit this collective behavior and indicate its potential to be a selective pressure across ecological contexts.

Developing a new Phylogeny-driven Random Forest Model for Functional Metagenomics.

Metagenomics is an unobtrusive science linking microbial genes to biological functions or environmental states. Classifying microbial genes into their functional repertoire is an important task in the downstream analysis of Metagenomic studies. The task involves Machine Learning (ML) based supervised methods to achieve good classification performance. Random Forest (RF) has been applied rigorously to microbial gene abundance profiles, mapping them to functional phenotypes. The current research targets tuning RF by the evolutionary ancestry of microbial phylogeny, developing a Phylogeny-RF model for functional classification of metagenomes. This method facilitates capturing the effects of phylogenetic relatedness in an ML classifier itself rather than just applying a supervised classifier over the raw abundances of microbial genes. The idea is rooted in the fact that closely related microbes by phylogeny are highly correlated and tend to have similar genetic and phenotypic traits. Such microbes behave similarly; and hence tend to be selected together, or one of these could be dropped from the analysis, to improve the ML process. The proposed Phylogeny-RF algorithm has been compared with state-of-the-art classification methods including RF and the phylogeny-aware methods of MetaPhyl and PhILR, using three real-world 16S rRNA metagenomic datasets. It has been observed that the proposed method not only achieved significantly better performance than the traditional RF model but also performed better than the other phylogeny-driven benchmarks (p < 0.05). For example, Phylogeny-RF attained a highest AUC of 0.949 and Kappa of 0.891 over soil microbiomes in comparison to other benchmarks.

The heterogeneity of microbial diversity and its drivers in two types of sediments from tidal flats in Beibu Gulf, China

Mudflats and sandflats are two common types of coastal tidal flats, the structure and function differences of microbial communities between them are still underappreciated. Beibu Gulf is a diurnal tidal regime located in China, the differences between the two type of tidal flats could be more distinct. In this study, we collected a total of 6 samples from Beibu Gulf, consisting of 3 sandflats samples and 3 mudflats samples, classified based on clay and silt content. Generally, the mudflats samples exhibited higher levels of NH4+_N and TOC, but lower in ORP and pH. The microbial diversity of the two types of tidal flats was investigated, revealing great differences existed and sandflats had higher microbial richness and diversity than mudflats. Furthermore, we analyzed the association between microbial communities and environmental factors, finding NH4+_N to have the highest contribution to the total variation in microbial community structure, and microbial groups such as Desulfobacterota, Campilobacterota, Chloroflexota, Calditrichota, Spirochaetota, Zixibacteria, Latescibacterota and Sva0485 group in mudflats were positively associated with NH4+_N. The functions of microbial community were predicted using metagenomic sequences and metagenome assembled genome (MAG). Mudflats contained more genes for carbon fixation. Nitrate and nitrite reduction were widely existed in mudflats and sandflats, but nitrogen fixation was only existed in mudflats, and Campilobacterota, Desulfobacterota and Gammaproteobacteria MAGs were mainly responsible for it. Sandflats composed more genes for ammonium oxidation, but no MAG was found whether in sandflats or mudflats. Microbes in mudflats exhibited a greater abundance of genes related to sulfur cycling, especially in reduction process, unique MAGs in mudflats such as Calditrichota, Chloroflexota, Desulfobacterota and Zixibacteria MAGs are responsible for sulfate and sulfite reduction. Finally, we predicted functions of ammonium related microbes in mudflats based on MAGs and found Campilobacterota and Desulfobacterota MAGs were important for high accumulation of ammonium in mudflats. This study illuminated the structural and functional differences of microbial communities in mudflats and sandflats, providing new insights into the relationship of microbial communities and environment in the tidal flat.

Insight into microbial functional genes’ role in geochemical distribution and cycling of uranium: The evidence from covering soils of uranium tailings dam

There exists a research gap on microbial functional genes’ role in U geochemical behavior and cycling in U contaminated soils, which has been poorly understood. Herein, 16S rRNA sequencing gene amplifiers and metagenome analysis were applied to probe microbial community structure and functional metabolism of different depth layers of covering soils in U tailings dam. Results showed that the soils were highly enriched with U (47.5–123.3 mg/kg) and a remarkable portion of 35–70% was associated with the labile fractions. It was found that U geochemical distribution was notably interacted with functional genes from N, S, Fe and P related microbes. Importantly, diminution in gene NirK and amplification in nrfH involving in nitrate reduction could induce microbial tolerance to U. Moreover, gene Sat in microbial sulfate reduction, NosZ and NorB in nitrate reduction, phnD, upgA and upgC in P transportation and phnI, phnK, phoA and opd in microbial organic P mineralization, were all closely linked to U geochemical distribution, species and cycling. All these findings disclose the functional genes that may control the transfer and transformation behavior of U in soil environment, which provides important and novel indications for the bio-remediation strategies towards U polluted sites.

Assembling the anaerobic gamma-butyrobetaine to TMA metabolic pathway in Escherichia fergusonii and confirming its role in TMA production from dietary L-carnitine in murine models.

The key atherosclerotic TMAO originates from the initial gut microbial conversion of L-carnitine and other dietary compounds into TMA. Developing therapeutic strategies to block gut microbial TMA production needs a detailed understanding of the different production mechanisms and their relative contributions. Recently, we identified a two-step anaerobic pathway for TMA production from L-carnitine through initial conversion by some microbes into the intermediate γBB which is then metabolized by other microbes into TMA. Investigational studies of this pathway, however, are limited by the lack of single microbes harboring the whole pathway. Here, we engineered E. fergusonii strain to harbor the whole two-step pathway and optimized the expression through cloning a specific chaperone from the original host. Inoculating germ-free mice with this recombinant E. fergusonii is enough to raise serum TMAO to pathophysiological levels upon L-carnitine feeding. This engineered microbe will facilitate future studies investigating the contribution of this pathway to cardiovascular disease.