Microbial Ecology Research Articles

Submucosal Microbiome Profiles inPaired and Unpaired Samples From Healthy and Peri-Implantitis Dental Implants.

This cross-sectional study aimed to compare the composition of the submucosal microbiome of peri-implantitis with paired and unpaired healthy implant samples. We evaluated submucosal plaque samples obtained in 39 cases, including 13 cases of peri-implantitis, 13 cases involving healthy implants from the same patient (paired samples), and 13 cases involving healthy implants from different individuals (unpaired samples). The patients were evaluated using next-generation genomic sequencing (Illumina) based on 16S rRNA gene amplification. The sequences were grouped according to the amplicon sequence variant (ASV) to define the taxonomic categories. Alpha diversity was analyzed using Shannon's and Simpson's indices, while beta diversity was evaluated using principal coordinate analysis, analysis of similarities, and permutational multivariate variance analysis. Additionally, UniFrac distances were evaluated using Quantitative Insights into Microbial Ecology 2. Finally, we evaluated between-group differences in the taxonomic components. There were no significant between-group differences in alpha diversity. The average bacterial ratios of Filifactor alocis, Porphyromona endodontalis, Tannerella forsythia, Treponema denticola, Peptostreptococcaceae [Eubacterium nodatum], Desulfobulbus sp. HTM 041, and Mogibacterium timidum significantly differed between peri-implantitis samples and unpaired samples from the healthy implants (p < 0.05). However, there were few differences in the microbiota between peri-implantitis samples and those paired with healthy implants in the same patient. Future studies comparing the microbiome compositions using sequencing techniques between healthy implants and implants with peri-implantitis should focus on retrieving samples from the same patient, especially in individuals with a history of periodontitis.

Exploring strategies for kitchen waste treatment and remediation from the perspectives of microbial ecology and genomics.

Nowadays, the rapid growth of population has led to a substantial increase in kitchen waste and wasted sludge. Kitchen waste is rich in organic matter, including lignocellulose. Synergistic treatment involving kitchen waste and wasted sludge can enhance treatment process. Vermicomposting can facilitate microbial activities on organic matter. Nevertheless, the underlying mechanisms remain unclear. In this study, metagenomics was used to analyze microbial functional genes in vermicomposting. Redundancy analysis found that TOC, TN and DTN adversely affect earthworm growth and reproduction. The relative abundance of Bacteroidetes and Firmicutes increased with earthworms, thereby potentially augmenting lignocellulose degradation. The predominant functional genes included amino acid, carbohydrate, and inorganic ion conversion and metabolism. Metagenomics analysis demonstrated that GH1, GH3, GH5, GH6, GH9, GH12, GH44, GH48 and GH74, GT41, GT4, GT2, and GT51 were dominant. Furthermore, there was higher abundance of carbohydrate-active enzymes in the vermicomposting, particularly during the later phases (30-45 days). Co-occurrence network revealed that Cellvibrio in the vermicomposting exhibited a relatively dense positive correlation with other microbial groups. The findings elucidated the mechanism of vermicomposting as a promising approach for managing kitchen waste and wasted sludge.

Gene abundance and microbial syntrophy as key drivers of anaerobic digestion revealed through 16S rRNA gene and metagenomic analysis.

Genes in microorganisms influence the biological processes in anaerobic digestion (AD). However, key genes involved in the four metabolic steps (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) remain largely unexplored. This study investigated the abundance and distribution of key functional genes in full-scale anaerobic digesters processing food waste (FWDs) and municipal wastewater (MWDs) through 16S rRNA gene and shotgun metagenomic analysis. Our results revealed that FWDs exhibited a higher abundance of key genes in the metabolic steps, despite having significantly lower microbial diversity compared to MWDs. Pathways and genes associated with syntrophic oxidation of acetate (SAO) and butyrate (SBO) were more present in FWDs. SAO potentially used both the conventional reversed Wood-Ljungdahl pathway and its integration with the glycine cleavage system in FWDs, which complements pathways for acetate oxidation under ammonia stress conditions. Similarly, genes associated with SBO (atoB and croR) were notably more prevalent in FWDs compared to MWDs with an 8.4-fold and 108-fold increase, respectively, indicating the adaptation of SBO bacteria to convert butyrate into acetate. The higher abundance of key genes in FWDs was driven by microbes adapting to the feedstock compositions with higher levels of substrate content, volatile fatty acids, and ammonia. This study quantified the genes central to AD metabolism and uncovered the contributions of microbial diversity, gene abundance, syntrophy, and feedstock characteristics to the functionality of AD processes. These findings enhance understanding of the microbial ecology in AD and provide a foundation for developing innovative strategies to enhance biogas production and waste management.

Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility.

The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.

P-426. Antimicrobial Resistance Focus in French ICU: A national surveillance network analysis on ventilator acquired pneumonia

Abstract Background The aim of this study was to perform a characterization of patients who underwent mechanical ventilation, the incidence rate of ventilator acquired pneumoniae (VAP) as well as identification of the pathogens involved, their resistance profiles, and the associated clinical outcomes. This group will be scrutinized for patterns and outcomes specifically associated with ventilator use. Cumulative incidence of VAP Methods Adult patients undergoing mechanical ventilation hospitalized in France for at least 48 hours in ICU participating to REA-REZO surveillance network between 2018 and 2021 were included in this cohort. To estimate the cumulative incidence of VAP, extubation and death were considered as competing event. Description of the cohort Results In this cohort, 98 047 patients were included. Among them, 12 251 (12.5%) had a VAP; the incidence rate for 1000 ventilation days was 18.9 cases per 1000 ventilation days. The median age of the cohort is 66 [55-75] years old with a male predominance (63.0 %). The SAPS score is 49 [36-63], the mortality is 24.4 % and the median ICU length of stay is 7 [4-15] days. Ventilated patients are more frequently admitted for medical (63.0 %) compared to surgical (37.0%) reason. At day 30, the attributable mortality associated with ventilator-associated pneumonia (VAP) was estimated at 4.9% (3.7% - 6.2%). Out of 15,575 diagnosed cases of VAP, there were 4,695 instances of polymicrobial VAP, which constitutes 30.1% of the cases. Non-fermenting Gram-negative bacteria were a significant group, contributing to 25.4% of the VAP cases, with Pseudomonas aeruginosa being the most significant contributor (3 924 cases, 76.2% of non-fermenters) Description of the microbial ecology of VAP Conclusion The development of VAP is frequent, especially in patients admitted for medical reasons, with high severity and appears to be associated with an increased use of medical devices, like urinary and central venous catheters, reflecting the complexity of their clinical management. Disclosures Xavier Bourge, PharmD, MSD France: Employee Arnaud Friggeri, MD, MSD France: Advisor/Consultant Alain Lepape, MD, MSD France: Grant/Research Support Claire Prevot, n/a, MSD France: Employee Anais Machut, n/a, MSD France: Grant/Research Support Charles-Hervé Vacheron, MD, MSD France: Grant/Research Support

Editorial: FEMS EC Thematic Issue "Aquatic Microbial Ecology".

High relative abundance of yeast (Vishniacozyma, Papiliotrema, and Filobasidium) and bacterial (Massilia) genera found in spinach seeds correlates with suppression of Globisporangium ultimum damping-off infection.

Isolation and Identification of Hydrocarbon-Degrading Bacteria from Diesel-Contaminated Soils

Aim: To Isolate, screen and identify bacterial species with hydrocarbon biodegradative potentials from diesel-polluted soils using redox indicator (2% v/v of 2,6 – dichlorophenol indophenols- DCPIP) and Turbidity measurements. Place and Duration of Study: Microbiology laboratory in the Department of Environmental Management and Toxicology, Federal University of Petroleum Resources, Effurun, between 2022 and 2024. Methodology: Soil samples from diesel-contaminated site were collected from diesel mechanic workshop, analysed using the spread plate isolation technique on Bushnell Haas mineral salt agar selective medium, were screened for Bacterial species with hydrocarbon degradative potential using the redox indicator (2% v/v of 2,6 – dichlorophenol indophenols- DCPIP) and Turbidity measurement. Selected Bacterial isolates were used for the hydrocarbon degradation studies, were characterized based on biochemical tests and identified with the aid of the Biolog database and 16S rRNA gene sequencing techniques. Results: Eight diesel degrading Bacteria species were identified, belonging to the following genera; Acinetobacter, Klebsiella, and Pseudomonas. Among these, the four most potent degraders were identified as Acinetobacter rudis (M2712942.1), Acinetobacter bereziniae (MT111619.1), Pseudomonas koreensis (MW794239.1), and Klebsiella aerogenes (CP070520.1) and the % diesel reduction achieved in 15 days were; 70%, 48%, 47% and 45%, while the % Turbidity increase were 84%, 79%, 78% and 76% respectively. Consequently, the partial 16S rRNA gene sequences revealed the two most potent diesel degrading bacterial strains were Acinetobacter rudis and Acinetobacter bereziniae with 70% and and 48% respectively. Conclusion: These findings demonstrate the potential of indigenous bacteria for effective bioremediation of petroleum-contaminated environments. The study provides critical insights into sustainable solutions for mitigating hydrocarbon pollution, contributing to advancements in environmental microbiology and ecosystem restoration.

Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life

The microbiome of dairy calves undergoes extensive change due to various forces during the first weeks of life. Importantly, diseases such as bovine respiratory disease (BRD) and calf diarrhea can have profound impacts on the early-life microbiome. Therefore, a longitudinal, repeated-measures pilot study was designed to characterize the establishment of nasal and fecal microbiomes of dairy calves, assess the governing forces of microbial assembly, and evaluate how disease states impact these microbial ecologies. Dairy calves (n = 19) were clinically evaluated for gastrointestinal and respiratory disease across three weeks beginning at age ≤ seven days old. Fecal (n = 57) and nasal (n = 57) microbial samples were taken for paired-end 16S rRNA gene amplicon sequencing. Taxonomy and diversity analyses were used to characterize early-life nasal and fecal microbiomes. Stochasticity and determinism were measured using normalized stochasticity testing (NST) and Dirichlet multinomial model (DMM). All analyses were tested for statistical significance. Clinical diarrhea was observed in 11 of the 19 calves. Clinical BRD was not independently observed among the cohort; however, two calves presented clinical signs of both BRD and diarrhea. Taxonomic analysis revealed that fecal samples were highlighted by Bacteroidaceae (40%; relative abundance), Ruminococcaceae (13%), and Lachnospiraceae (10%), with changes in diversity (Kruskal–Wallis; p &lt; 0.05) and composition (PERMANOVA; p &lt; 0.05). Clinical diarrhea reduced diversity in the fecal microbiome but did not impact composition. Nasal samples featured Moraxellaceae (49%), Mycoplasmataceae (16%), and Pasteurellaceae (3%). While no diversity changes were seen in nasal samples, compositional changes were observed (p &lt; 0.05). NST metrics (Kruskal–Wallis; p &gt; 0.01) and DMM (PERMANOVA; p &lt; 0.01) revealed that stochastic, neutral theory-based assembly dynamics govern early-life microbial composition and that distinct microbial populations drive community composition in healthy and diarrheic calves.

Fecal microbiota is more stable during degradation and more diverse for ex situ cheetahs in Namibia compared to the USA

The relationships between gut microbiota and animal health are an important consideration increasingly influential in the management of wild and ex situ endangered species, such as the cheetah (Acinonyx jubatus). To better understand these relationships, fresh fecal samples are currently required as a non-invasive alternative for the gut microbiome. Unfortunately, fresh samples are challenging to collect in the wild. This study had two aims: 1) to determine the optimal collection time point for cheetah feces after deposit in their native environment of Namibia as a guide for wild cheetah fecal microbiome studies; and 2) to compare the fecal microbiota of two ex situ cheetah populations (Front Royal, VA, USA and Otjiwarongo, Namibia), which also consume different diets. We collected eight fresh fecal samples from cheetahs in Namibia and allowed them to decompose for four days, taking subsamples each day. The fresh Namibian samples (n = 8) were also used in objective two for comparison to fresh USA cheetah samples (n = 8). All samples were analyzed for bacterial community diversity and composition using 16S rRNA gene amplicon sequencing. First, over a five-day sampling period in Namibia, subsamples 1-3 days post-fresh showed no changes in bacterial diversity or composition compared to fresh subsamples. Second, fresh ex situ cheetah samples under Namibian conditions had increased bacterial taxa, more phylogenetically diverse bacterial communities, and compositionally distinct microbiomes from cheetahs managed in human care in the USA. However, when bacterial ASVs were weighted by relative abundance, both populations shared 69% of their total bacterial sequences indicating a conserved cheetah microbiota between the two populations. We also found few differences in predictive functions of the fecal microbiota between the populations, where only one disease-related pathway was higher in the USA samples. Overall, our findings suggest that in dry season conditions (no recorded rainfall) in Namibia, fecals may be usable for up to three days after defecation for microbial ecology studies. There are significant differences between ex situ Namibian and USA populations, and we suggest further investigation into the influence of diet, host demographics, and environment on the gut microbiota and health of cheetahs.

Genetic and species rearrangements in microbial consortia impact biodegradation potential.

Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the reorganisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.

Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.

One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.

MATRIX: a platform for cultivation profiling and bioactive discovery in natural product research

The MATRIX protocol presents a novel miniaturized 24-well plate approach for microbial cultivation profiling, enabling the efficient and parallel assessment of microbial metabolite production. This method integrates a media MATRIX within a microbioreactor to facilitate the creation of diverse growth conditions for microbial cultivation. The 24-well format supports the simultaneous study of multiple microbial strains and conditions, allowing the discovery of novel bioactive compounds. By employing a variety of media compositions and cultivations, MATRIX enhances the understanding of microbial metabolic pathways and interactions. This protocol provides a robust platform for natural product discovery, microbial ecology studies, and drug development, showcasing its potential to uncover new natural products and other valuable bioactives. The MATRIX approach offers a resource-efficient platform for microbial biodiscovery, contributing significantly to natural product research and drug development.

The influence of depth on the global deep-sea plasmidome

Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270–1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea’s microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.

Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches.

Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.

The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes.

Designing microbiomes for applications in health, bioengineering, and sustainability is intrinsically linked to a fundamental theoretical understanding of the rules governing microbial community assembly. Microbial ecologists have used a range of mathematical models to understand, predict, and control microbiomes, ranging from mechanistic models, putting microbial populations and their interactions as the focus, to purely statistical approaches, searching for patterns in empirical and experimental data. We review the success and limitations of these modeling approaches when designing novel microbiomes, especially when guided by (inevitably) incomplete experimental data. Although successful at predicting generic patterns of community assembly, mechanistic and phenomenological models tend to fall short of the precision needed to design and implement specific functionality in a microbiome. We argue that to effectively design microbiomes with optimal functions in diverse environments, ecologists should combine data-driven techniques with mechanistic models - a middle, third way for using theory to inform design.

Microbial ecology of sandflies—the correlation between nutrition, Phlebotomus papatasi sandfly development and microbiome

The role and the impact of the microbial component on the biology, ecology, and development of sandflies is largely unknown. We evaluated the impact of larval nutrition on laboratory-reared sandflies in correlation to the abundance of food, light starvation, and food with/without live microbiome, by monitoring the survival and development of immature stages, and the longevity of adult sandflies. Within this study we examined 360 larvae, 116 pupae, and 120 adult flies of Phlebotomus papatasi for the microbial gut content. The data showed that the presence of a live and diverse microbiome plays a role in the development and survival of larvae. The mortality rate of the larvae was higher, and larval development was longer for sandflies maintained on microbiome-depleted medium, in comparison to the larvae fed with medium containing alive and complex microbiome. Actively feeding larvae reduce microbial abundance and diversity of the medium. The microbial content of the larval gut depends on the composition of the rearing medium, indicating a potential attraction to certain bacteria. The microbial content of the pupa gut was severely diminished, with overall survival of two bacterial species in adult insects - Ochrobactrum intermedium (found in 95% of dissected adults) and Bacillus subtilis (16%). Further microbial studies may aid in developing biological control methods for sandfly larval or adult stages.

Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.

Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the fecal microbiota and gut pH every two hours. We detected strong diurnal rhythms in both microbial alpha- and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.

Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples

Abstract The field of microbial ecology is increasingly recognizing the need for methods to isolate and culture gut microbes to better understand how these microorganisms impact animal physiology, especially in mammalian hosts. Currently, there is a lack of clear methods to store microbial samples for cultivability, especially when samples are collected from the field, transported to the laboratory, and preserved under long-term storage for weeks to months compared to mere days in the biomedical field. Here, the cecal contents of groundhogs (Marmota monax) were processed and stored with or without various preservation solutions at −80 °C for at least 2 months. All microbial samples were then grown in distinct nutrient media in liquid and plate conditions and were incubated under anaerobic and aerobic environments. Treatment comparisons revealed that the samples stored in preservation solutions containing 1 or more cryoprotectants provided the greatest and most consistent bacterial densities. To test the long-term storage efficacy of the preservation solutions, we inventoried taxonomic identities and abundances of these cultures using 16S rRNA amplicon sequencing. Our findings highlight that: (1) preserved samples containing cryoprotectants exhibited the highest microbial richness and diversity and resembled the original cecal samples the most when grown under anaerobic conditions; and (2) the effect of individual animal identity was detectable in the membership of cultured communities, irrespective of preservation solutions. Our study is the first to demonstrate the importance of preservation solutions containing multiple cryoprotectants for long-term storage and further microbial culturing and novel isolation. Understanding and improving storage methods that preserve microbial physiology and conserve their compositional diversity is essential for field-collected samples useful in mammalian microbiome and culturomics studies, promoting a better comprehension of the identity and function of wild host-associated microbiomes.

The use of Mahad leaf pellet feed affects the fermentation process and rumen micro-biota in beef cattle

Abstract The study’s objective was to assess how Mahad leaf pellet feed affected the microbial ecology and rumen fermentation in beef cattle. Using a 4×4 Latin square design, 4 Brahman crossbred heifers weighing 250 ± 40 kg (1–1.5 years old) were randomly allocated to each of the following treatments: The powder for concentration in the experiment following: (1) Control (0 g concentrate powder), (2) 50 g concentrate powder, (3) 100 g concentrate powder, and (4) 150 g concentrate powder. The cows received ad libitum rice straw and concentrate at 1% BW. None of the treatments affected ruminal temperature, NH 3 -N, microbial protein production, or pH. Hematocrit (Hct) and blood urea N were unaffected by the addition of Mahad leaf pellet feed. On the other hand, the addition of Mahad leaf pellet feed to the diet led to a linear reduction in the ruminal concentration of acetic acid (P = 0.01) and an increase in the ruminal concentration of propionic acid (P = 0.02). We projected a decrease in ruminal CH 4 production (P = 0.02) as the amount of Mahad leaf pellet feed in the diet increased. The addition of Mahad leaf pellet feed to the diet resulted in a linear decrease in the protozoal population (P = 0.01) as the amount increased. According to the current study, Mahad leaf pellet feed alters ruminal fermentation by reducing the acetate-to-propionate ratio and estimating the amount of CH 3 produced. It has no influence on ruminal pH, microbial synthesis or blood parameters. Decreases in the ruminal protozoa may account for some of the changes in ruminal fermentation parameters. The ideal level for animal feed supplementation is 150 g of the total ration, as supplementing beyond 150 g of the concentrate portion did not significantly enhance these beneficial effects.

Antibiotic Resistance Patterns of Pseudomonas aeruginosa in Clinical Specimens from Khartoum Hospitals, Sudan

Background: One of the most common causes of nosocomial infection is Pseudomonas aeruginosa. Antimicrobial resistance has expanded globally as a result of profound changes in microbial genetic ecology caused by the indiscriminate use of antimicrobials. Objective: The aim of study was to determine the antibiotic resistance pattern of Pseudomonas aeruginosa isolated from clinical specimens. Materials and Methods: The present study used purposive sampling as the sampling technique. Pseudomonas aeruginosa isolated from 77 clinical specimens, Susceptibility Test was determined using Kirby-Bauer Disk Diffusion. Results: The results revealed that and the isolated organism test is Pseudomonas aeruginosa was isolated from all the clinical Specimen by 100%, The results revealed that the frequencies of Cefpodoxime antibiotics for the Urine 32.4% (11/31) was sensitive, while 58.8% (20/31) was resistant., for the wound 20.6% (7/34) was sensitive, while 79.4% (27/34) was resistant., for the Ear 5.9% (2/12) was sensitive, while 29.4% (10/12) was resistant. Resistant average for cefpodoxime was 74.0%, and there is a high statistically significant relation between Cefpodoxime antibiotics and samples (Urine and wound) and a normal relation with Ear. Conclusion: Drug resistance in P. aeruginosa is a multifactorial increasing phenomenon. Estimated frequencies were between 12-36%. Mechanisms of resistance either through membrane permeability and efflux system or through its virulence factors or acquired genetically by plasmid. Combination of these mechanisms leads to a superbug, which is very difficult to be treated.