Evaluating the use of diversity indices to distinguish between microbial communities with different traits

Protocol for identifying Mycobacterium tuberculosis infection status through airway microbiome profiling

This protocol describes the steps to determine an airway microbiome signature for identifying Mycobacterium tuberculosis infection status. We outline procedures for processing microbiome data, calculating diversity measures, and fitting Dirichlet multinomial mixture models. Additionally, we provide steps for analyzing taxonomic relative and differential abundances, as well as identifying potential biomarkers associated with infection status. For complete details on the use and execution of this protocol, please refer to Kayongo et al.1.

Oral microbiome profiles of gingivitis and periodontitis by next-generation sequencing among a group of hospital patients in Korea: A cross-sectional study

OBJECTIVES

The oral microbiome plays an important role in the development and progression of periodontal disease. The purpose of this study was to compare microbial profiles of oral cavities in good health, with gingivitis, and in a state of periodontitis, and to identify novel pathogens involved in periodontal diseases.

METHODS

One hundred and two participants, including 33 healthy controls, 41 patients with gingivitis, and 28 patients with periodontitis, were included in this cross-sectional study. Salivary oral microbiomes were investigated using 16S rRNA metagenomic sequencing, and the microbial profiles of each group were compared using age- and sex-adjusted general linear models.

RESULTS

The abundance of amplicon sequence variants and Chao1 diversity were significantly elevated in the gingivitis and periodontitis groups relative to healthy controls (p = 0.046). Based on linear discriminant analysis (LDA) scores (>2), Tenericutes, Mollicutes, Mycoplasmatales, Mycoplasmataceae, Mycoplasma, Bacteroidaceae, and Phocaeicola were significantly enriched in the gingivitis group, and Synergistetes, Synergistia, Synergistales, Synergistaceae, Fretibacterium, Sinanaerobacter, and Filifactor were enriched in the periodontitis group. The relative abundances of Fretibacterium fastidiosum, Sinanaerobacter chloroacetimidivorans, and Filifactor alocis (q = 0.008, all bacteria) were highest in the periodontitis group and lowest in the control group. The relative abundance of Treponema denticola was significantly elevated in the periodontitis group compared to the other two groups (q = 0.024).

CONCLUSIONS

Oral microbiomes differed between groups. T. denticola, F. fastidiosum, S. chloroacetimidivorans and F. alocis were significantly more abundant in the periodontitis group than in the control group. Additionally, the abundance of T. denticola and F. fastidiosum in the periodontitis group was significantly different from that in the gingivitis group.

Symbiotic fungi alter plant resource allocation independent of water availability

PREMISE

The ability of plants to adapt or acclimate to climate change is inherently linked to their interactions with symbiotic microbes, notably fungi. However, it is unclear whether fungal symbionts from different climates have different impacts on the outcome of plant-fungal interactions, especially under environmental stress.

METHODS

We tested three provenances of fungal inoculum (originating from dry, moderate or wet environments) with one host plant genotype exposed to three soil moisture regimes (low, moderate and high). Inoculated and uninoculated plants were grown in controlled conditions for 151 days, then shoot and root biomass were weighed and fungal diversity and community composition determined via amplicon sequencing.

RESULTS

The source of inoculum and water regime elicited significant changes in plant resource allocation to shoots versus roots, but only specific inocula affected total plant biomass. Shoot biomass increased in the high water treatment but was negatively impacted by all inoculum treatments relative to the controls. The opposite was true for roots, where the low water treatment led to greater proportional root biomass, and plants inoculated with wet site fungi allocated significantly more resources to root growth than dry- or moderate-site inoculated plants and the controls. Fungal communities of shoots and roots partitioned by inoculum source, water treatment, and the interaction of the two.

CONCLUSIONS

The provenance of fungi can significantly affect total plant biomass and resource allocation above- and belowground, with fungi derived from more extreme environments eliciting the strongest plant responses.

Sulfate and Dissolved Organic Carbon Concentrations Drive Distinct Microbial Community Patterns in Prairie Wetland Ponds

Prairie wetland ponds on the Great Plains of North America offer a diverse array of geochemical scenarios that can be informative about their impact on microbial communities. These ecosystems offer invaluable ecological services while experiencing significant stressors, primarily through drainage and climate change. In this first study systematically combining environmental conditions with microbial community composition to identify various niches in prairie wetland ponds, sediments had higher microbial abundance but lower phylogenetic diversity in ponds with lower concentrations of dissolved organic carbon ([DOC]; 10-18 mg/L) and sulfate ([SO4 2-]; 37-58 mg/L) in water. As [DOC] and [SO4 2-] increased, there was an initial decline in abundance but not phylogenetic diversity. Maximum values of both abundance and phylogenetic diversity occurred between 56 and 115 mg/L [DOC] and 5,000-6,000 mg/L [SO4 2-] and decreased thereafter in ponds with 150-180 mg/L and 8,000-14,000 mg/L [DOC] and [SO4 2-], respectively. These findings confirm that environmental variables shape the microbial communities and that key microbial taxa involved in sulfur and carbon cycling dominated these ponds potentially impacting vital biogeochemical processes such as bioavailability of heavy metals, carbon sequestration, and methane emissions.

Important ecophysiological roles of Nocardiopsis in lignocellulose degradation during aerobic compost with humic acid addition

Improving lignocellulose degradation and organic matter conversion in agricultural and livestock wastes remains a great challenge. Here, the contribution of humic acid (HA) to lignocellulose degradation was investigated, focusing on the abundance of key microbial species and carbohydrate-active enzymes during aerobic composting. The results demonstrated that the addition of HA not only increased the complexity of the microbial network, but also enhanced the positive interaction between microorganism. The abundance of phylum Actinobacteria related to lignin degradation was significantly increased, especially genus Nocardiopsis (50.97 %), and Nocardiopsis was significantly positively correlated with HA and humus (HS) (p < 0.05). Additionally, the abundance of GH (43.45%) and AA (5.88%) enzymes and the activation of metabolic pathways of AA, carbohydrates and energy were significantly increased (p < 0.05). Remarkably, the quantity of lignocellulose-degrading genes and carbohydrate-active enzymes experienced a marked boost (p < 0.05), with the peak abundance observed in Nocardiopsis. The structural equation model revealed that the addition of HA boosted the abundance of Nocardiopsis, which in turn amplified lignocellulose degradation by up-regulating lignocellulose degradation genes and enhancing carbohydrase activity, and facilitating the conversion of HA and FA. The lignocellulose degradation experiment verified that Nocardiopsis alba exhibited good ability in the degradation of cellulose and hemicellulose. These findings provided a novel perspective on the mechanisms underlying lignocellulose degradation, and broaden the understanding of the ecophysiological role of Nocardiopsis in composting system.

Development of a clinical metagenomics workflow for the diagnosis of wound infections

BACKGROUND

Wound infections are a common complication of injuries negatively impacting the patient's recovery, causing tissue damage, delaying wound healing, and possibly leading to the spread of the infection beyond the wound site. The current gold-standard diagnostic methods based on microbiological testing are not optimal for use in austere medical treatment facilities due to the need for large equipment and the turnaround time. Clinical metagenomics (CMg) has the potential to provide an alternative to current diagnostic tests enabling rapid, untargeted identification of the causative pathogen and the provision of additional clinically relevant information using equipment with a reduced logistical and operative burden.

METHODS

This study presents the development and demonstration of a CMg workflow for wound swab samples. This workflow was applied to samples prospectively collected from patients with a suspected wound infection and the results were compared to routine microbiology and real-time quantitative polymerase chain reaction (qPCR).

RESULTS

Wound swab samples were prepared for nanopore-based DNA sequencing in approximately 4 h and achieved sensitivity and specificity values of 83.82% and 66.64% respectively, when compared to routine microbiology testing and species-specific qPCR. CMg also enabled the provision of additional information including the identification of fungal species, anaerobic bacteria, antimicrobial resistance (AMR) genes and microbial species diversity.

CONCLUSIONS

This study demonstrates that CMg has the potential to provide an alternative diagnostic method for wound infections suitable for use in austere medical treatment facilities. Future optimisation should focus on increased method automation and an improved understanding of the interpretation of CMg outputs, including robust reporting thresholds to confirm the presence of pathogen species and AMR gene identifications.

Gut Microbiome Alteration in HIV/AIDS and the Role of Antiretroviral Therapy-A Scoping Review

(1) Background: The gut microbiota plays a crucial role in chronic immune activation associated with human immunodeficiency virus (HIV) infection, acquired immune deficiency syndrome (AIDS) pathogenesis, non-AIDS-related comorbidities, and mortality among people living with HIV (PLWH). The effects of antiretroviral therapy on the microbiome remain underexplored. This study aims to map the evidence of the impact of integrase strand transfer inhibitors (INSTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) on the gut microbiota of PLWH. (2) Methods: A scoping review was conducted using PubMed, Web of Science, and Embase, with reports collected following PRISMA for Scoping Reviews (PRISMA-ScR). (3) Results: Evidence suggests that INSTI-based regimes generally promote the restoration of alpha diversity, bringing it closer to that of seronegative controls, while beta diversity remains largely unchanged. INSTI-based therapies are suggested to be associated with improvements in microbiota composition and a tendency toward reduced inflammatory markers. In contrast, NNRTI-based treatments demonstrate limited recovery of alpha diversity and are linked to an increase in proinflammatory bacteria. (4) Conclusions: Based on the review of the current literature, it is indicated that INSTI-based antiretroviral therapy (ART) therapy facilitates better recovery of the gut microbiome.

Changes in the taxonomic composition of soil bacterial communities under different inter-row tillage managements in a sloping vineyard of the Balaton Uplands (Hungary)

The common grape (Vitis vinifera L.) has been cultivated for thousands of years. Nowadays, it is cultivated using a variety of tillage practices that affect the structure of the soil microbial communities and thus the health of the vine. The aim of this study was to explore and compare the effects of tillage (shallow tillage with bare soil) and no-tillage (perennial grass cover) practices on soil physical and chemical properties and soil bacterial community diversities in a small catchment. Soil samples were taken in July and October 2020 at different slope positions of two vineyards exposed to erosion. The two sampling sites were separated by the agricultural inter-row management type: tilled and no-tilled slopes. The taxonomic diversity of bacterial communities was determined using 16S rRNA gene-based amplicon sequencing method on Illumina MiSeq platform. Based on the examined soil properties, the sampling areas were separated from each other according to the positions of the upper and lower slopes and the sampling times. Both the tilled and no-tilled soil samples were dominated by sequences assigned to phyla Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Gemmatimonadota. The results showed that tillage had no significant effect compared to the no-tilled samples in the studied area. Water runoff and seasonally changed soil physical and chemical properties affected mainly the bacterial community structures.

Assessment of Antimicrobial Therapy in Eradicating Chlamydia muridarum in Research Mice: Immune Status and its Impact on Outcomes

Chlamydia muridarum (Cm) is a moderately prevalent, gram-negative, intracellular bacterium that affects laboratory mice, causing subclinical to severe disease, depending on the host's immune status. The effectiveness of various antibiotic regimens aimed at eradicating Cm in both immunodeficient and immunocompetent laboratory mice was evaluated. NSG mice were cohoused with Cm-shedding BALB/cJ mice for 14 days to simulate natural exposure. Four groups of 8 infected NSG mice were treated for 7 days with either 0.08% sulfamethoxazole and 0.016% trimethoprim (TMS) in water, 0.0625% doxycycline in feed, 0.124%/0.025% TMS in feed, or 0.12% amoxicillin in feed. A control group was provided standard water and feed. The impact of treatment on gastrointestinal microbiota (GM) was performed using next-generation shotgun sequencing on the last day of treatment. TMS and Amoxicillin had negligible effects on GM, while doxycycline had the largest effect. All antibiotic treated NSG mice exhibited clinical disease, including dehydration, hunched posture, >20% weight loss, and dyspnea, leading to euthanasia 21-40 days post-treatment (32.6 ± 4.2 days; mean ± SD). Untreated controls were euthanized 14-33 days post-exposure (23.75 ± 5.9 days). All mice were fecal PCR positive for Cm at euthanasia. Histological evaluation revealed multifocal histiocytic and neutrophilic bronchointerstitial pneumonia and/or bronchiolitis featuring prominent intralesional chlamydial inclusion bodies in all mice. Subsequently, groups of 8 C57BL/6J, BALB/cJ, NOD.SCID, and NSG mice infected with Cm were treated with 0.124%/0.025% TMS in feed for 7 (BALB/cJ and C57BL/6J) or 21 days (NSG and NOD.SCID). All immunocompetent and NOD.SCID mice were negative for Cm by PCR 14 days post-treatment, remained clinically normal and had no evidence of Cm infection at necropsy, all NSG mice remained Cm positive and were euthanized. While these findings highlight the difficulties in eradicating Cm from highly immunodeficient mice, eradication of Cm from immunocompetent or moderately immunocompromised mice with antibiotics is feasible.

Enhance PD/A biofilm formation via a novel biochar/tourmaline modified-biocarriers to treat low-strength contaminated surface water: Initial adhesion and high-substrate microenvironment

In this work, a novel polyurethane carrier modified with biochar and tourmaline/zeolite powder at ratio of 1:1 and 1:2 was developed to promote the formation of biofilms and the synergy of overall bacterial activity for Partial Denitrification/Anammox to treat low-nitrogen contaminated surface water. Based on the batch experiment, the modified biocarrier, BTP2 (biochar: tourmaline = 2: 1), exhibited the highest total nitrogen removal efficiency (83.63%) under influent total nitrogen of 15 mg/L and COD/NO3- of 3. The dense biofilm was formed in inner side of biocarrier owing to the increased surface roughness and various functional groups suggested by scanning electron microscopy and Fourier-transform infrared analysis. The EPS content increased from 200.15 to 220.26 mg/g VSS in BTP2 system. Besides, the rapid NH4+ capture and organics release of the modified carrier fueled the growth of anammox and denitrification bacteria, with the activity of 2.13 ± 0.52 mg N/gVSS/h and 6.70 ± 0.52 mg N/gVSS/h (BTP2). High-throughput sequencing unraveled the increased abundances of Candidatus_Competibacter (0.82%), Thauera (0.60%) and Candidatus_Brocadia (0.55%) which was responsible for the synergy of incomplete reduction of NO3- to NO2- and NH4+ oxidation. Overall, this study provided a valid and simple-control guide for biofilm formation towards rapid enrichment and great collaboration of Anammox and denitrification bacteria.

Deciphering microbial communities of three Savoyard raw milk cheeses along ripening and regarding the cheese process

Different Savoyard cheeses are granted with PDO (Protected Designation or Origin) and PGI (Protected Geographical Indication) which guarantees consumers compliance with strict specifications. The use of raw milk is known to be crucial for specific flavor development. To unravel the factors influencing microbial ecosystems across cheese making steps, according to the seasonality (winter and summer) and the mode of production (farmhouse and dairy factory ones), gene targeting on bacteria and fungus was used to have a full picture of 3 cheese making technologies, from the raw milk to the end of the ripening. Our results revealed that Savoyard raw milks are a plenteous source of biodiversity together with the brines used during the process, that may support the development of specific features for each cheese. It was shown that rinds and curds have very contrasted ecosystem diversity, composition, and evolution. Ripening stage was selective for some bacterial species, whereas fungus were mainly ubiquitous in dairy samples. All ripening stages are impacted by the type of cheese technologies, with a higher impact on bacterial communities, except for fungal rind communities, for which the technology is the more discriminant. The specific microorganism's abundance for each technology allow to see a real bar-code, with more or less differences regarding bacterial or fungal communities. Bacterial structuration is shaped mainly by matrices, differently regarding technologies while the influence of technology is higher for fungi. Production types showed 10 differential bacterial species, farmhouses showed more ripening taxa, while dairy factory products showing more lactic acid bacteria. Meanwhile, seasonality looks to be a minor element for the comprehension of both microbial ecosystems, but the uniqueness of each dairy plant is a key explicative feature, more for bacteria than for fungus communities.

Effect of oral tryptamines on the gut microbiome of rats-a preliminary study

Background

Psilocybin and related tryptamines have come into the spotlight in recent years as potential therapeutics for depression. Research on the mechanisms of these effects has historically focused on the direct effects of these drugs on neural processes. However, in addition to such neural effects, alterations in peripheral physiology may also contribute to their therapeutic effects. In particular, substantial support exists for a gut microbiome-mediated pathway for the antidepressant efficacy of other drug classes, but no prior studies have determined the effects of tryptamines on microbiota.

Methods

To address this gap, in this preliminary study, male Long Evans rats were treated with varying dosages of oral psilocybin (0.2 or 2 mg/kg), norbaeocystin (0.25 or 2.52 mg/kg), or vehicle and their fecal samples were collected 1 week and 3 weeks after exposure for microbiome analysis using integrated 16S ribosomal DNA sequencing to determine gut microbiome composition.

Results

We found that although treatment with neither psilocybin nor norbaeocystin significantly affected overall microbiome diversity, it did cause significant dose- and time-dependent changes in bacterial abundance at the phylum level, including increases in Verrucomicrobia and Actinobacteria, and decreases in Proteobacteria.

Conclusion and Implications

These preliminary findings support the idea that psilocybin and other tryptamines may act on the gut microbiome in a dose- and time-dependent manner, potentially identifying a novel peripheral mechanism for their antidepressant activity. The results from this preliminary study also suggest that norbaeocystin may warrant further investigation as a potential antidepressant, given the similarity of its effects to psilocybin.

Exploring the Association between Anxiety, Depression, and Gut Microbiota during Pregnancy: Findings from a Pregnancy Cohort Study in Shijiazhuang, Hebei Province, China

Negative emotions and gut microbiota during pregnancy both bear significant public health implications. However, the relationship between them has not been fully elucidated. This study, utilizing data from a pregnancy cohort, employed metagenomic sequencing to elucidate the relationship between anxiety, depression, and gut microbiota's diversity, composition, species, and functional pathways. Data from 87 subjects, spanning 225 time points across early, mid, and late pregnancy, were analyzed. The results revealed that anxiety and depression significantly corresponded to lower alpha diversity (including the Shannon entropy and the Simpson index). Anxiety and depression scores, along with categorical distinctions of anxiety/non-anxiety and depression/non-depression, were found to account for 0.723%, 0.731%, 0.651%, and 0.810% of the variance in gut-microbiota composition (p = 0.001), respectively. Increased anxiety was significantly positively associated with the abundance of Oscillibacter sp. KLE 1745, Oscillibacter sp. PEA192, Oscillibacter sp. KLE 1728, Oscillospiraceae bacterium VE202 24, and Treponema socranskii. A similar association was significantly noted for Oscillibacter sp. KLE 1745 with elevated depression scores. While EC.3.5.3.1: arginase appeared to be higher in the anxious group than in the non-anxious group, vitamin B12-related enzymes appeared to be lower in the depression group than in the non-depression group. The changes were found to be not statistically significant after post-multiple comparison adjustment.

Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach

Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg-1) like Cu (0.009-0.01), Ni (0.005-0.002), Mn (0.078-0.056), Cr (0.015-0.009), Pb (0.008-0.006), Zn (0.225-0.086), Fe (2.124-0.764), Al (3.477-22.277), and Ti (99.792-45.012) along with high content of chlorophenol, and lignin. The comparative analysis of organic pollutants in sediment samples using gas chromatography-mass spectrometry (GC-MS) revealed the presence of major highly refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc in sediment samples which are reported as a potential toxic compounds. Simultaneously, high-throughput sequencing targeting the V3-V4 hypervariable region of the 16S rRNA genes, resulted in the identification of 1,249 and 1,345 operational taxonomic units (OTUs) derived from a total of 115,665 and 119,386 sequences read, in PPS-1 and PPS-2, respectively. Analysis of rarefaction curves indicated a diversity in OTU abundance between PPS-1 (1,249 OTUs) and PPS-2 (1,345 OTUs). Furthermore, taxonomic assignment of metagenomics sequence data showed that Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), and Planctomycetes (5.40%; 4.70%) were the most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), and Gammaproteobacteria were the most recorded classes in PPS-1 and PPS-2, respectively. At the genus level, Thiobacillus (7.60%; 4.50%) was the most abundant genera grown in sediment samples. The results indicate significant differences in both the diversity and relative abundance of taxa in the bacterial communities associated with PPS-2 when compared to PPS-1. This study unveils key insights into contaminant characteristics and shifts in bacterial communities within contaminated environments. It highlights the potential for developing efficient bioremediation techniques to restore ecological balance in pulp-paper mill waste-polluted areas, stressing the importance of identifying a significant percentage of unclassified genera and species to explore novel genes.

Alpha Diversity Indices as Indicators of the Variability of Gut Microbiota in Obese Adolescents of Different Ethnicities

We compared alpha diversity indices of the intestinal microbiota in adolescents with obesity and normal body weight, taking into account their ethnicity. Intestinal biocenosis was studied by metasequencing of amplicon libraries of V3-V4 fragments of the 16S rRNA gene. The alpha diversity of the microbiota was assessed using classical and alternative indices. Statistically significant differences in intestinal microbiota were observed between Russians with obesity and Buryats with normal body weight, as well as between Russians with obesity and Buryats with obesity when assessing the Shannon-Weaver, Chao1 indices, Faith phylogenetic diversity index, ACE, Fisher, Gini coefficient, Margalef, and Menkhinik indices. It was shown that alpha diversity indices can be used to assess significance of differences and variability of the intestinal microbiota in multifactorial diseases such as obesity in adolescents; however, the scope of application of the criteria should be considered.

Assessment of DNA extraction methods for human gut mycobiome analysis

The gut mycobiome plays an important role in the health and disease of the human gut, but its exact function is still under investigation. While there is a wealth of information available on the bacterial community of the human gut microbiome, research on the fungal community is still relatively limited. In particular, technical methodologies for mycobiome analysis, especially the DNA extraction method for human faecal samples, varied in different studies. In the current study, two commercial kits commonly used in DNA extraction, the QIAamp® Fast DNA Stool Mini Kit and DNeasy PowerSoil Pro Kit, and one manual method, the International Human Microbiome Standards Protocol Q, were compared. Furthermore, the effectiveness of two different bead-beating machines, the Mini-Beadbeater-16 and FastPrep-24TM 5G, was compared in parallel. A mock fungal community with a known composition of fungal strains was also generated and included to compare different DNA extraction methods. Our results suggested that the method using the DNeasy PowerSoil Pro Kit and Mini-Beadbeater-16 provides the best results to extract DNA from human faecal samples. Based on our data, we propose a standard operating procedure for DNA extraction from human faecal samples for mycobiome analysis.

Early life gut microbiome in children following spontaneous preterm birth and maternal preeclampsia

The early life microbiome plays an important role in developmental and long-term health outcomes. However, it is unknown whether adverse pregnancy complications affect the offspring's gut microbiome postnatally and in early years. In a longitudinal cohort with a five-year follow-up of mother-child pairs affected by preeclampsia (PE) or spontaneous preterm birth (sPTB), we evaluated offspring gut alpha and beta diversity as well as taxa abundances considering factors like breastfeeding and mode of delivery. Our study highlights a trend where microbiome diversity exhibits comparable development across adverse and normal pregnancies. However, specific taxa at genus level emerge with distinctive abundances, showing enrichment and/or depletion over time in relation to PE or sPTB. These findings underscore the potential for certain adverse pregnancy complications to induce alterations in the offspring's microbiome over the course of early life. The implications of these findings on the immediate and long-term health of offspring should be investigated in future studies.

Influence of the Antibiotic Oxytetracycline on the Morphometric Characteristics and Endophytic Bacterial Community of Lettuce (Lactuca sativa L.)

Antibiotics enter the soil with compost prepared from livestock manures and other sources. There is concern that they may influence plant growth and cause antibiotic resistance in soil and plant endospheric microbiomes. In the present work, lettuce plants were cultivated in soil and hydroponics spiked with oxytetracycline (0, 15, and 300 mg × kg-1 and 0, 15, and 50 mg × L-1, respectively) during a 28-day greenhouse experiment. It was revealed that the antibiotic reduced the chlorophyll content, the biomass, and the length of the roots and stems by 1.4-4.7, 1.8-39, 2.5-3.2, and 1.8-6.3 times in soil and in hydroponics. The copy numbers of the tet(A) and tet(X) genes were revealed to be 4.51 × 103-1.58 × 105 and 8.36 × 106-1.07 × 108 copies × g-1, respectively, suggesting the potential migration of these genes from soil/hydroponics to plant roots and leaves. According to a non-metric multidimensional scaling (NMDS) analysis of the 16S rRNA amplicon sequencing data, endospheric bacterial communities were similar in leaves and roots independent of the growing substrate and antibiotic concentration. While soil bacterial communities were unaffected by the presence of antibiotics, hydroponic communities exhibited dependency, likely attributable to the absence of the mitigating effect of soil particle absorption.

Gut microbiota changes in animal models of spinal cord injury: a preclinical systematic review and meta-analysis

BACKGROUND

An increasing number of studies show that the intestinal flora is closely related to spinal cord injury. Many researchers are exploring the changes in the richness, diversity, and evenness of intestinal flora in spinal cord injury animal models to identify the characteristic bacteria.

METHODS

A comprehensive literature search was conducted using three databases: PubMed, Embase, and Web of Science. A meta-analysis was performed using R 4.3.1 to evaluate the comparison of microbiota diversity, richness, and evenness and the relative abundance of intestinal microbiota in animals with spinal cord injury and blank controls.

RESULTS

Fifteen studies were included in the meta-analysis, of which 12 involved gut microbiota distribution indicators and 11 included intestinal microflora relative abundance indicators. Meta-analysis of high-dimensional indicators describing the distribution of the gut microbiota identified a substantial decline in the evenness and richness of the intestinal flora. In addition, the Actinobacteria phylum and Erysipelotrichales and Clostridiales orders were significantly different between the spinal cord injury and sham groups; therefore, they may be the characteristic bacteria in spinal cord injury models.

CONCLUSION

Our meta-analysis suggested that the gut microbiota in the spinal cord injury animal model group was altered compared with that in the control group, with varying degrees of changes in richness and evenness and potentially pathogenic characteristic flora. More rigorous methodological studies are needed because of the high heterogeneity and limited sample size. Further research is needed to clinically apply intestinal microbiota and potentially guide fecal microbiota transplantation therapy.

The Immunomodulatory Effect of β-Glucan Depends on the Composition of the Gut Microbiota

This study aimed to elucidate the relationship between the immunomodulatory effects of β-glucan and the composition of gut microbiota in mice. The mice were fed a diet containing β-glucan for 3 weeks, and feces, blood, and tissues were then collected to analyze the immunomodulatory effect and gut microbiota composition. Based on the results of the analysis of the expression level of immune-associated proteins, the high immunomodulatory effect group (HIE) and low immunomodulatory effect group (LIE) were categorized. Before the β-glucan diet, the proportions of the phylum Bacteroidota, family Muribaculaceae, and family Lactobacillaceae were significantly higher in HIE than in LIE. Furthermore, the genus Akkermansia was absent before the β-glucan diet and increased after β-glucan diet. These microbes had the ability to metabolize β-glucan or were beneficial to health. In conclusion, our findings demonstrate that variation in the composition of gut microbiota among individuals can result in varying expressions of β-glucan functionality. This outcome supports the notion that β-glucan may be metabolized through diverse pathways by gut microbes originally possessed by mice, subsequently producing various metabolites, such as short-chain fatty acids. Alternatively, the viscosity of the intestinal mucosa could be enhanced by β-glucan, potentially promoting the growth of certain bacteria (e.g., the genus Akkermansia). This study provides insights into the intricate interplay between β-glucan, gut microbiota, and immunomodulation.

Microbial Diversity Using a Metataxonomic Approach, Associated with Coffee Fermentation Processes in the Department of Quindío, Colombia

Coffee fermentation is a complex process, mainly involving bacteria and yeasts, whose interaction influences beverage quality. The way this process is conducted affects the interactions between these microorganisms. To identify microbial diversity in fermenting coffee, samples were collected from 20 farms in the Department of Quindío, Colombia. Metataxonomic analyses using high-throughput sequencing and volatile organic compound identification in green coffee beans were performed with HS-SPME and GC-MS. Potential relationships between some families and genera with different fermentation types and coffee quality were evaluated. In our results, samples presented with high richness and diversity were greater for bacteria than for yeast/fungi. The Enterobacteriaceae family dominated at the beginning of fermentation, while Leuconostoc, Lactobacillus, Gluconobacter, and Acetobacter genera dominated at the end, a finding related to pH reduction and final coffee quality. Overall, 167 fungal families were identified, but Saccharomyceaceae dominated from the beginning. Alcohols and esters were the main chemical classes identified in green coffee bean samples from these fermentations. These results will facilitate the identification process conditions that influence the presence and abundance of microorganisms related to quality as well as contributing to the design of strategies to conduct fermentations to improve the final quality of coffee.

Enhanced nitrogen removal in mainstream deammonification systems at ambient temperature by novel modified carriers and differentiation of microbial community transformation

Zeolite-modified polyurethane (ZP) carriers and zeolite/tourmaline-modified polyurethane (ZTP) carriers were proposed to enhance mainstream deammonification. The system with ZTP carriers was rapidly established in 28 days with a nitrogen removal rate (NRR) of 0.150 kg N·(m³·d)^-1. Moreover, the facilitative effect of tourmaline was suggested by the highest humic acid peak intensity and more balanced potential activity. Besides, SEM-EDS analysis revealed carrier characteristic improvement was achieved in both novel carriers while maintaining an excellent spatial structure. Moreover, the microbial analysis suggested that both modified carriers support the substrate supply to anaerobic ammonium oxidizing bacteria (AnAOB) by enhancing dissimilatory nitrate reduction to ammonium and partial denitrification under nitrate accumulation conditions. Nevertheless, the ZTP system had a greater advantage over maintaining the original AnAOB (Candidatus Jettenia) and ammonium oxidizing bacteria (Nitrosomonas) abundance. Overall, this study provides ZTP carriers with great potential for facilitating the establishment of mainstream deammonification at full-scale WWTPs.

Impact of HLA-B27 and Disease Status on the Gut Microbiome of the Offspring of Ankylosing Spondylitis Patients

Multiple studies have shown the microbiota to be abnormal in patients with spondyloarthritis (SpA). The purpose of this study was to explore the genetic contributions of these microbiota abnormalities. We analyzed the impact of HLA-B27 on the microbiota of children at risk for SpA and compared the microbiota of HLA-B27+ pediatric offspring of ankylosing spondylitis (AS) patients with that of HLA-B27+ children with SpA. Human DNA was obtained from the offspring for determination of HLA-B27 status and polygenic risk score (PRS). Fecal specimens were collected from both groups for sequencing of the V4 region of the 16S ribosomal RNA gene. Among the offspring of AS patients, there was slight clustering by HLA-B27 status. After adjusting for multiple comparisons, five operational taxonomic units (OTUs) representing three unique taxa distinguished the HLA-B27+ from negative children: Blautia and Coprococcus were lower in the HLA-B27+ offspring, while Faecalibacterium prausnitzii was higher. HLA-B27+ offspring without arthritis were compared to children with treatment-naïve HLA-B27+ SpA. After adjustments, clustering by diagnosis was present. A total of 21 OTUs were significantly associated with diagnosis state, including Bacteroides (higher in SpA patients) and F. prausnitzii (higher in controls). Thus, our data confirmed associations with B. fragilis and F. prausnitzii with juvenile SpA, and also suggest that the mechanism by which HLA-B27 is associated with SpA may not involve alterations of the microbiota.

Effect of g-C3N4 on biodiversity and structure of bacterial community in sediment of Xiangjiang River under tetracycline pressure

Photocatalysts have been widely prepared and used in wastewater treatment. Although the influence of photocatalyst application on survival and activity of organisms has been examined, its impact on composition and diversity of microbial community is not fully understood. In this study, the impact of photocatalyst g-C₃N₄ (Graphitic carbon nitride) on microbial communities in riverbed sediments polluted by antibiotic tetracycline (TC) was investigated. The sediment samples collected from the Xiangjiang River of China were exposed to different concentrations of TC, g-C₃N₄ and TC/g-C₃N₄ and the bacterial community were analyzed by Illumina sequencing. The results showed that the dominant bacterial phyla were Acidobacteriota, Proteobacteria, Actinobacteriota, and Chloroflexi in the study site. When compared to the control treatments, the application of TC, g-C₃N₄ and TC/g-C₃N₄ exhibited distinguishable effects on bacterial community structure in sediments. The presence of TC had greater influence on bacterial composition, while g-C₃N₄ and TC/g-C₃N₄ had less influence on bacteria. The diversity and richness of microorganisms in sediment increased under g-C₃N₄ application and reached the highest values when g-C₃N₄ was 75 mg/kg. The photocatalyst g-C₃N₄ restored bacterial community diversity affected by TC, reduced the TC residues in aquatic environment, and eliminated the side effects of TC application in sediments. Our study indicated that g-C₃N₄ was an environmentally friendly photocatalyst with lightly negative effects on microbial community in riverbed sediments, and could be used for effective remediation of TC-contaminated environments.

Phosphate functionalized iron based nanomaterials coupled with phosphate solubilizing bacteria as an efficient remediation system to enhance lead passivation in soil

Bioremediation technology has attracted increasing interest due to it efficient, economical and eco-friendly to apply to heavy metal contaminated soil. This study presents a new biological remediation system with phosphate functionalized iron-based nanomaterials and phosphate solubilizing bacterium strain Leclercia adecarboxylata. Different phosphate content functionalized iron-based nanomaterials were prepared, and nZVI@C/P1 (nP: nFe: nC=1:10:200) with high passivation efficiency was selected to combine with PSB for the remediation experiments. The change in lead fraction and microbial community under five conditions (CK, PSB, nZVI@C, nZVI@C/P1, nZVI@C/P1 + PSB) during 10 days incubation were investigate. The results indicated that nZVI@C/P1 + PSB increased the residual fraction of lead by 93.94% compared with the control group. Meanwhile, inoculation of Leclercia adecarboxylata became the dominant microflora in the soil microbial community during the remediation time, improving the utilization rate of phosphate in nZVI@C/P1 and enhancing the passivation efficiency of lead. Experimental findings demonstrated that combining nZVI@C/P1 with PSB could be considered as an efficient strategy for the lead contaminated soil remediation.

Anaerobic treatment of glutamate-rich wastewater in a continuous UASB reactor: Effect of hydraulic retention time and methanogenic degradation pathway

To investigate the anaerobic treatment efficiency and degradation pathways of glutamate-rich wastewater under various hydraulic retention times (HRTs), a lab-scale upflow anaerobic sludge blanket (UASB) reactor was operated continuously for 180 days. Results showed that high chemical oxygen demand (COD) removal efficiencies of 95.5%-96.5% were achieved at HRTs of 4.5 h-6 h with a maximum methane yield of 0.31 L-CH₄/g-COD. When the HRT was shortened to less than 3 h, the removal performance of the reactor declined. There also was an excessive accumulation of volatile fatty acids, which implies that an appropriately small HRT is applicable to the UASB reactor treating glutamate-rich wastewater. Methanogenic degradation of glutamate in the UASB reactor depended on the HRT applied, and the typical methane-producing capability of the sludge at an HRT of 3 h, in descending order, was acetate > glutamate > butyrate > H₂/CO₂ > valerate > propionate. Clostridium and Methanosaeta were predominant in the glutamate-degrading sludge. At least three degradation pathways most likely existed in the UASB reactor, and the pathway via 3-methlaspartate by Clostridium pascui was expected to be dominant.

Performance and microbial community variations of a upflow anaerobic sludge blanket (UASB) reactor for treating monosodium glutamate wastewater: Effects of organic loading rate

To investigate the effect of the organic loading rate (OLR) on anaerobic treatment of monosodium glutamate (MSG) wastewater, a lab-scale up-flow anaerobic blanket (UASB) reactor was continuously operated over a 222-day period. The overall performances of COD removal and methane recovery initially exhibited an increase and subsequently decreased when the OLR was increased from 1 g-COD/L/d to 24 g-COD/L/d. At the optimal OLR of 8 g-COD/L/d, superior performance was obtained with a maximum COD removal efficiency of 97%, a methane production rate of 2.3 L/L/d, and specific methanogenic activity of 86 mg-CH₄/g-VSS/d (feeding on glutamate), with superior characteristics of sludge in VSS concentration, average diameter of granules, and settling velocity. According to the results of the specific methanogenic activity, the methanogenic pathway was more inclined to pass through acetate than through hydrogen. Methanosarcina instead of Methanosaeta, with Methanobacterium and greatly increased Firmicutes, dominated in the UASB reactor after long term operation. These results support that the OLR had a substantial effect on both the treatment and energy recovery efficiency of MSG wastewater as well as on microbial community variations in the UASB reactor.

Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities

The disease of freshwater sponges was first discovered in 2011, when pink samples were found in the Central Basin of Lake Baikal. Subsequently, the visible signs of the disease have changed, and now sponges appear with various symptoms of damage to the body, such as discoloration, tissue necrosis, the formation of brown patches and dirty-purple biofilms on some branches. These signs of the disease are accompanied by the mass death of sponges. We identified differences in microbiomes by sequencing 16S rRNA genes and found changes in the consortium of microorganisms of freshwater Baikal sponges. We found that the observed imbalance in the studied microbial communities of diseased sponges is caused by several different conditionally pathogenic microorganisms that increase their negative effect by acting together and in concert, which leads to the death of photosynthetic microalgae and sponges. Sponges are an important component of coastal communities, and the massive loss of sponges can obviously affect the structure of benthic communities and the purity of water.