Hasil untuk "Microbial ecology"

M. Lynch, J. Neufeld

J. Stegen, Xueju Lin, A. Konopka et al.

J. G. Leahy, R. Colwell

The ecology of hydrocarbon degradation by microbial populations in the natural environment is reviewed, emphasizing the physical, chemical, and biological factors that contribute to the biodegradation of petroleum and individual hydrocarbons. Rates of biodegradation depend greatly on the composition, state, and concentration of the oil or hydrocarbons, with dispersion and emulsification enhancing rates in aquatic systems and absorption by soil particulates being the key feature of terrestrial ecosystems. Temperature and oxygen and nutrient concentrations are important variables in both types of environments. Salinity and pressure may also affect biodegradation rates in some aquatic environments, and moisture and pH may limit biodegradation in soils. Hydrocarbons are degraded primarily by bacteria and fungi. Adaptation by prior exposure of microbial communities to hydrocarbons increases hydrocarbon degradation rates. Adaptation is brought about by selective enrichment of hydrocarbon-utilizing microorganisms and amplification of the pool of hydrocarbon-catabolizing genes. The latter phenomenon can now be monitored through the use of DNA probes. Increases in plasmid frequency may also be associated with genetic adaptation. Seeding to accelerate rates of biodegradation has been shown to be effective in some cases, particularly when used under controlled conditions, such as in fermentors or chemostats.

D. Stahl, Berdena Flesher, H. Mansfield et al.

J. Russell, J. Rychlik

Donglin Wu, Lei Zhang, Zhanhe Zhang et al.

ABSTRACT: Sodium butyrate (SB) is a common feed additive used in calf nutrition to support early growth and gastrointestinal health; however, its long-term programming effects remain poorly characterized. This study examined the dose-dependent effects of preweaning SB supplementation in milk on long-term growth, metabolic profiles, and gastrointestinal microbiota in dairy cattle. Eighty Holstein calves were assigned to one of 4 treatments beginning at 2 to 4 d of age: milk supplemented with 0 (CON), 4.4 (LSB), 8.8 (MSB), or 17.6 (HSB) g/d of SB. The same animals were evaluated later as heifers at 15 mo of age for performance, metabolic parameters, and microbial communities. Ruminal fluid, fecal, and plasma samples were collected from 8 animals per group and analyzed via 16S rRNA sequencing (V3–V4 regions) and liquid chromatography-tandem MS–based metabolomics. The HSB group showed a significant reduction in withers height compared with CON, although no significant differences were detected in BW, heart girth, or reproductive measures. Metabolomic and biochemical profiling indicated disrupted sterol metabolism and signs of hepatic stress in HSB heifers, reflected by increased alanine aminotransferase and total bilirubin, alongside decreased total cholesterol and creatine. Ruminal microbiota in the HSB group exhibited reduced diversity, richness, and evenness, accompanied by a decline in beneficial bacteria such as Rikenellaceae_RC9_gut_group. Predicted microbial function indicated inhibited steroid biosynthesis in the rumen. In contrast, the intestinal microbiota composition remained largely unchanged, though steroid degradation function was suppressed. Correlation and network analyses linked these changes, suggesting that early high-dose SB disrupts ruminal microbial ecology, resulting in lasting impairments in host metabolic health and growth. Key biomarkers included Rikenellaceae_RC9_gut_group, steroid biosynthesis, and plasma creatine. Collectively, these results indicate that milk-supplemented high-dose SB in early life leads to long-term inhibitory effects on growth and metabolic homeostasis in dairy heifers, largely mediated through rumen microbiota-driven alterations in sterol metabolism.

Rebecca J. Case, Y. Boucher, I. Dahllöf et al.

L. Hugerth, Anders F. Andersson

Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.

H. Daims, Sebastian Lücker, M. Wagner

Lucía Schmidt-Santiago, David Rodríguez-Temporal, Carlos Sevilla-Salcedo et al.

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has become a cornerstone technology in clinical microbiology, enabling rapid and accurate microbial identification. However, the development of data-driven diagnostic models remains limited by the lack of sufficiently large, balanced, and standardized spectral datasets. This study investigates the use of deep generative models to synthesize realistic MALDI-TOF MS spectra, aiming to overcome data scarcity and support the development of robust machine learning tools in microbiology. We adapt and evaluate three generative models, Variational Autoencoders (MALDIVAEs), Generative Adversarial Networks (MALDIGANs), and Denoising Diffusion Probabilistic Model (MALDIffusion), for the conditional generation of microbial spectra guided by species labels. Generation is conditioned on species labels, and spectral fidelity and diversity are assessed using diverse metrics. Our experiments show that synthetic data generated by MALDIVAE, MALDIGAN, and MALDIffusion are statistically and diagnostically comparable to real measurements, enabling classifiers trained exclusively on synthetic samples to reach performance levels similar to those trained on real data. While all models faithfully reproduce the peak structure and variability of MALDI-TOF spectra, MALDIffusion obtains this fidelity at a substantially higher computational cost, and MALDIGAN shows competitive but slightly less stable behaviour. In contrast, MALDIVAE offers the most favorable balance between realism, stability, and efficiency. Furthermore, augmenting minority species with synthetic spectra markedly improves classification accuracy, effectively mitigating class imbalance and domain mismatch without compromising the authenticity of the generated data.

Reiji Suzuki, Takaya Arita

We propose a model for the evolutionary ecology of words as one attempt to extend evolutionary game theory and agent-based models by utilizing the rich linguistic expressions of Large Language Models (LLMs). Our model enables the emergence and evolution of diverse and infinite options for interactions among agents. Within the population, each agent possesses a short word (or phrase) generated by an LLM and moves within a spatial environment. When agents become adjacent, the outcome of their interaction is determined by the LLM based on the relationship between their words, with the loser's word being replaced by the winner's. Word mutations, also based on LLM outputs, may occur. We conducted preliminary experiments assuming that ``strong animal species" would survive. The results showed that from an initial population consisting of well-known species, many species emerged both gradually and in a punctuated equilibrium manner. Each trial demonstrated the unique evolution of diverse populations, with one type of large species becoming dominant, such as terrestrial animals, marine life, or extinct species, which were ecologically specialized and adapted ones across diverse extreme habitats. We also conducted a long-term experiment with a large population, demonstrating the emergence and coexistence of diverse species.

Satoyoshi Ishizaki, Tetsuo I. Kohyama, Yuki Ota et al.

Abstract Plant–microbe interactions in the phyllosphere provide invaluable information on plant ecology, with implications for ecosystem functioning and plant–atmosphere feedbacks. The composition of phyllosphere microbes varies significantly depending on host lineages, geographic regions, and climatic conditions. However, the factors driving these variations in interactions with plants remain poorly understood. Biogenic volatile organic compounds (BVOCs) emitted by plants may be important in these interactions. Here, we quantified the composition of phyllosphere microbial communities and terpene emissions from leaves of Japanese cedar (Cryptomeria japonica) trees grown in two common gardens from cuttings collected from natural populations across Japan. Amplicon sequencing revealed that microbial communities differed significantly between gardens and among host populations. Analysis of BVOC profiles showed that the camphene and total terpene emission rates were associated with bacterial composition, whereas that of ent-kaurene was marginally linked to fungal composition. The relative abundances of certain fungal genera that include the species reported to cause disease in Japanese cedar, the emission rates of most monoterpenes and a sesquiterpene β-farnesene were correlated with the climatic conditions at the origin sites of the cedar trees. These findings highlight the intricate relationships between phyllosphere microbes and terpene emission from host trees and suggest the role of climatic factors in shaping these associations.

Ole Martin Drevland, Eric J. de Muinck, Pål Trosvik et al.

Abstract Background The pivotal role of microbes in drug metabolism is increasingly recognized, as variation in the gut microbiome composition between individuals has been shown to impact systemic drug exposure, efficacy and toxicity. Mycophenolate mofetil (MMF) is a cornerstone in immunosuppressive therapy following solid organ transplantation. However, dosing and tolerance are challenged by significant pharmacokinetic variability among patients, largely due to variable degrees of enterohepatic recirculation of mycophenolic acid (MPA), the active moiety of MMF. It is hypothesized that the variability in MPA recirculation is driven by gut microbiome-derived β-glucuronidase (β-GUS) mediated cleavage of MPA-glucuronide (MPAG) excreted in the bile. Here, we investigated the bidirectional interaction between MPA and the gut microbiome in kidney transplant recipients, using a combination of in vivo and in vitro data. Results We compared the fecal microbiomes of kidney transplant recipients (n = 21) both pre- and post-transplantation to healthy individuals (n = 15) using shotgun metagenomic sequencing. We also determined the individual microbiome-derived reactivation rate of MPAG to MPA and show a strong positive correlation between this reactivation rate and the degree of MPA enterohepatic recirculation in vivo. Through metagenomic analysis, the reactivation rate of MPA was linked to specific gut microbial species. In particular, specific β-GUS gene variants associated with Faecalibacterium prausnitzii showed a strong impact on the conversion of MPAG to MPA. Furthermore, our study confirmed a significant shift in microbial composition post-transplantation and revealed notable fluctuations in species such as F. prausnitzii and Akkermansia muciniphila across different time points after transplantation. Lastly, we provide evidence that the microbiome-derived reactivation rate of MPA is linked to specific beta-glucuronidase alleles. Conclusions We highlight for the first time that the ex vivo determined reactivation rate of MPA explains the variation of enterohepatic recirculation, emphasizing the important role of F. prausnitzii in this process. More broadly, our findings suggest that the gut microbiome significantly influences the degree of enterohepatic recirculation of MPA, providing valuable insights that could be relevant for optimizing individualized immunosuppressive drug dosing in transplant patients. Video Abstract

Harry Lerner, Marcel Eck, Christoph Link et al.

Biodegradable plastics are an important component for achieving a circular polymer economy. To be considered biodegradable at the regulatory level, plastics must pass standardized tests, for example under industrial composting conditions at 58 °C (ISO 14855-1). Although such tests are frequently applied, little is known about the microorganisms catalyzing these degradation processes. Recently, bioplastics with properties similar to polyethylene, Long-Chain Aliphatic Polyesters (LCAP), for example polyester 1,18-octadecanediol-alt-1,18-octadecanedioic acid (abbreviated PE-18,18), were shown to biodegrade under industrial composting conditions. In this work, we analyzed the microbial communities that had developed in the compost treatments at the end of the biodegradation test for three different LCAPs (PE-18,18, PE-12,12 and PE-2,18) relative to the untreated controls, via amplicon-sequencing of bacterial 16S and fungal ITS2 rDNA. This revealed significant treatment-induced shifts in the bacterial communities (p < 0.05), with Pseudonocardia and Thermomonospora ASVs enriched in all LCAP-treated samples compared to the controls (p ≤ 0.0001), while no pronounced shifts were observed for the fungal community. Thermomonospora sequences showed high similarity to T. curvata DSM43183, which encodes the known polyester hydrolase Tcur1278, and the presence of gene tcur1278 was confirmed in LCAP-treated samples via PCR. Enzyme assays with heterologously expressed and partially purified Tcur1278 demonstrated its activity on PE-2,18 LCAP, releasing up to 230 μmol of soluble monomers over 48 h at 50 °C. Hence, our study implicated Thermomonospora species in LCAP degradation during thermophilic composting, based on taxonomic enrichment, and provided evidence linking the detected phylotypes to Tcur1278, the first bacterial enzyme demonstrated to depolymerize LCAP. It thereby is the first evidence for an ecological relevance of Tcur1278-encoding Thermomonospora phylotypes for bioplastic degradation in situ.

Yu Liu, Jingmei Ma, Xiang Li et al.

Abstract Background The early colonization and establishment of the microbiome in newborns is a crucial step in the development of the immune system and host metabolism. However, the exact timing of initial microbial colonization remains a subject of ongoing debate. While numerous studies have attempted to determine the presence or absence of intrauterine bacteria, the majority of them have drawn conclusions based on sequencing data from maternal or infant samples taken at a single time point. In this study, we aimed to investigate the microbial population in amniotic fluid (AF) from the second trimester until the time of delivery using multiple microbiological methods. Methods AF samples were collected during the second trimester (19–21 gestational weeks) and at the time of delivery. Cohort 1 included 51 women who underwent the term and elective cesarean section, with both their second trimester and delivery AF samples (n = 55, respectively) analyzed. Cohort 2 contained 22 women who experienced infection-related adverse pregnancy outcomes (including preterm birth, histological chorioamnionitis, and stillbirth), with only their second trimester AF samples (n = 24) examined. Additionally, multiple procedural negative controls and technical positive controls were applied to this study to remove potential contamination. Microbial profiles were assessed through cultivation, quantitative real-time polymerase chain reaction, 16S ribosomal RNA gene sequencing, and cytokine analysis. Results In cohort 1, the bacterial load and community structure in the second trimester AF samples were indistinguishable from negative controls. Although marginally higher bacterial loads and different bacterial communities were observed in the delivery AF samples compared to negative controls, these bacterial DNA were not considered biologically functional due to the absence of maternal inflammatory responses. In cohort 2, the bacterial load and community structure of the second trimester AF samples differed significantly from those of negative controls, with Ureaplasma and Lactobacillus identified as the most prevalent genera against negative controls. Conclusions Our study demonstrates that no microorganisms were detected in the AF of healthy pregnancies from the second trimester to the delivery. The presence of Ureaplasma and Lactobacillus in the second trimester AF may be associated with infection-related adverse pregnancy outcomes. Video Abstract

Yingchun Han, Zhaochao Deng, Yongyi Peng et al.

Abstract Background Reductive dehalogenation is crucial for halogen cycling and environmental remediation, yet its ecological role is not completely understood, especially in deep-sea environments. To address this gap, we investigated the diversity and expression of genes encoding reductive dehalogenase catalytic subunits (RdhAs), and ecophysiology of potential organohalide reducers in deep-sea cold seeps, which are environments rich in halogenated compounds. Results Through genome-resolved metagenomic analysis of 165 global cold seep sediment samples, 4 types of RdhA-like sequences were identified based on their features and phylogenetic relationships: prototypical respiratory, transmembrane respiratory, cytosolic, and a novel clade. Cold seeps were found to harbor a higher abundance of these rdhA-like genes compared to other marine sediments, highlighting their potential as microbial reductive dehalogenation hotspots. These rdhA-like genes are encoded by a wide range of microorganisms across 4 archaeal and 36 bacterial phyla, significantly expanding the known diversity of organohalide reducers. Halogen geochemistry, laboratory incubations, metatranscriptomic data, and metabolomic profiling confirmed the presence of organohalides at concentrations of up to 18 mg/g in these sediments and suggested the potential for microbial reductive dehalogenation. Our findings suggest that organohalide reducers in cold seep sediments may participate in diverse biogeochemical processes, as inferred from the presence of genes related to carbon, hydrogen, nitrogen, sulfur, and trace element cycling. Additionally, RdhA-like proteins from cold seeps have diverse N-terminal structures across different gene groups. Conclusions These findings collectively suggest that reductive dehalogenation is an important process in deep-sea environments, mediated by a diverse array of microbes and novel enzymes. The discovery of diverse and abundant rdhA-like genes, along with their genomic context and potential metabolic linkages, highlights the role of cold seeps as reservoirs of microbial diversity with possible implications for environmental remediation. Video Abstract

Wenzheng Guan, Tian Zhou, Jiao Jiao et al.

Abstract This study aims to evaluate differences in gut microbiota structures between infertile women undergoing frozen embryo transfer (FET) with gestational diabetes mellitus (GDM) and healthy controls (HCs), and to identify potential markers. We comprehensively enrolled 193 infertile women undergoing FET (discovery cohort: 38 HCs and 31 GDM; validation cohort: 85 HCs and 39 GDM). Gut microbial profiles of the discovery cohort were investigated during the pre-pregnancy (Pre), first trimester (T1), and second trimester (T2). The microbial community in the HCs group remained relatively stable throughout the pregnancy, while the microbial structure alteration occurred in the GDM group during T2. A model based on ten bacteria and ten metabolites simultaneously was used to predict the risk of GDM developing in the pre-pregnancy state with the ROC value of 0.712. Algorithms on the basis of marker species and biochemical parameters can be used as effective tools for GDM risk evaluation before pregnancy.

Widad Zernadji, Faten Rahmani, Sihem Jebri et al.

The microbiological safety of ready-to-eat (RTE) salads is considered as a major concern due to the absence of lethal treatments during processing. In this study, we aimed to investigate the microbiological quality of RTE salads commercialized in Tunisia and to determine the antibiotic resistance of isolated pathogens, in particular Staphylococcus aureus (S. aureus). A total of 100 samples were analyzed for total aerobic bacteria, total coliforms, Escherichia coli (E. coli), yeasts and molds, Salmonella spp., Listeria monocytogenes (L. monocytogenes), and S. aureus as well as norovirus (NoV) GI and GII using specific standard methods described by the International Organization for Standardization (ISO). All samples presented unacceptable microbiological quality due to high concentrations of total aerobic bacteria and yeasts (> 106 CFU/g) and total coliforms (> 104 CFU/g). E. coli and molds were detected at unsatisfactory levels in 4% and 12% of samples, respectively. The pathogens Salmonella spp. and L. monocytogenes were not detected. S. aureus were detected at unsatisfactory levels in 6% of samples. S. aureus isolates were resistant to more than five antibiotic classes. Thus, RTE salads could be a vehicle of multiresistant S. aureus. The total prevalence of NoV GII was 2% (mean 3.81±0.30 Log GC/25 g), and no NoV GI-positive samples were identified. This study showed that the microbiological quality of RTE salads commercialized in Tunisia was unacceptable, highlighting the need to ensure good agricultural and hygiene practices from farm to fork to improve the quality and safety of these products.

James A. Fellows Yates, I. Velsko, Franziska Aron et al.

Significance The microbiome plays key roles in human health, but little is known about its evolution. We investigate the evolutionary history of the African hominid oral microbiome by analyzing dental biofilms of humans and Neanderthals spanning the past 100,000 years and comparing them with those of chimpanzees, gorillas, and howler monkeys. We identify 10 core bacterial genera that have been maintained within the human lineage and play key biofilm structural roles. However, many remain understudied and unnamed. We find major taxonomic and functional differences between the oral microbiomes of Homo and chimpanzees but a high degree of similarity between Neanderthals and modern humans, including an apparent Homo-specific acquisition of starch digestion capability in oral streptococci, suggesting microbial coadaptation with host diet. The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.

Steven A. Wilbert, J. M. Mark Welch, G. Borisy

SUMMARY A fundamental question in microbial ecology is how microbes are spatially organized with respect to each other and their host. A test bed for examining this question is the tongue dorsum, which harbors a complex and important microbial community. Here, we use multiplexed fluorescence spectral imaging to investigate the organization of the tongue microbiome at micron to hundred-micron scales. We design oligonucleotide probes for taxa both abundant and prevalent, as determined by sequence analysis. Imaging reveals a highly structured spatial organization of microbial consortia, ranging in linear dimension from tens to hundreds of microns. The consortia appear to develop from a core of epithelial cells, with taxa clustering in domains suggestive of clonal expansion. Quantitative proximity analysis provides the basis for a model of tongue dorsum microbiome organization and dynamics. Our work illustrates how high-resolution analysis of micron-scale organization provides insights into physiological functions and microbiome-host interactions.