Hasil untuk "Microbial ecology"

M. Yuan, Xue Guo, Linwei Wu et al.

P. Louis, H. Flint

A. Ramette

Environmental microbiology is undergoing a dramatic revolution due to the increasing accumulation of biological information and contextual environmental parameters. This will not only enable a better identification of diversity patterns, but will also shed more light on the associated environmental conditions, spatial locations, and seasonal fluctuations, which could explain such patterns. Complex ecological questions may now be addressed using multivariate statistical analyses, which represent a vast potential of techniques that are still underexploited. Here, well-established exploratory and hypothesis-driven approaches are reviewed, so as to foster their addition to the microbial ecologist toolbox. Because such tools aim at reducing data set complexity, at identifying major patterns and putative causal factors, they will certainly find many applications in microbial ecology.

M. E. Davey, G. O’Toole

D. Savage

S. Socransky, A. Haffajee

D. Speth, Michiel H. in ‘t Zandt, Simon Guerrero-Cruz et al.

Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date. ANaerobic AMMonium OXidation (ANAMMOX) combined with partial nitritation has been adopted for removal of ammonium from wastewater. Here, Speth et al. describe the bacterial metagenome of a partial-nitritation/anammox (PNA) reactor, and provide 23 draft genomes, 19 of which were previously uncharacterized/sequenced/cultivated.

O. Paliy, Vijay Shankar

Pablo Gallardo Molina, Brian I. Choi, Michael Vanek et al.

ABSTRACT Urinary tract infections represent one of the most prevalent bacterial diseases, yet current diagnostic and research methodologies are hampered by inadequate culture media that fail to replicate the bladder biochemical environment. Conventional artificial urine formulations contain undefined components, lack essential nutrients, or inadequately support urinary microbiome (urobiome) growth. To address these limitations, we developed SimUrine, a fully defined synthetic urine medium that aims to replicate human bladder chemistry while supporting diverse microbial growth requirements. SimUrine was systematically developed through iterative optimization of multi-purpose artificial urine, incorporating defined concentrations of carbon sources, vitamins, trace elements, and amino acids within physiologically relevant ranges. The modular design enables component substitution without complete reformulation, facilitating customization for culturomics, antimicrobial susceptibility testing, and microbial ecology studies, while reducing batch-to-batch variability associated with authentic urine. Performance evaluation demonstrated SimUrine's capability to support the growth of fastidious urobiome members, including Lactobacillus species, Aerococcus urinae, and Corynebacterium riegelii, which fail to proliferate in conventional minimal media. Physicochemical characterization confirmed that SimUrine formulation exhibits properties within normal human urine ranges for density, conductivity, osmolarity, and viscosity, ensuring physiological relevance. Clinical applications revealed reduced antibiotic susceptibility compared to standard media, suggesting a more accurate representation of in vivo conditions. Co-culture experiments using Escherichia coli and Enterococcus faecalis demonstrated previously unobserved microbial interactions, highlighting SimUrine's utility for investigating urobiome dynamics. SimUrine represents a significant advancement in urobiome research methodology, providing a standardized, reproducible platform for investigating the urobiome under physiologically relevant conditions, potentially improving fundamental understanding and clinical diagnostic approaches.IMPORTANCEUrinary tract infections (UTIs) affect millions globally, yet current research and diagnostic methods rely on inadequate culture media that fail to replicate the bladder's unique biochemical environment. This fundamental limitation has hindered accurate UTI research and potentially compromised clinical treatment decisions. SimUrine addresses this critical gap as the first fully defined synthetic urine medium that mimics human bladder chemistry while supporting the growth of diverse urinary microbes. The breakthrough enables the cultivation of urobiome organisms in a minimal medium that resembles natural conditions, revealing novel microbial interactions that influence urinary health. Crucially, SimUrine demonstrates different antimicrobial susceptibility patterns compared to standard clinical media, suggesting current testing protocols may inaccurately predict treatment outcomes. This standardized, reproducible platform eliminates the variability of authentic urine samples while maintaining physiological relevance, potentially transforming urobiome research methodology and providing a new tool for the study of UTIs worldwide.

Vicente Gomez Herrera, Scott Weady

We develop and analyze a model for a flat microbial droplet growing on the surface of a three-dimensional viscous fluid. The model describes growth-induced stresses at the fluid surface, density variations in the bulk due to nutrient consumption, and the resulting fluid flows that arise. We reformulate this free-boundary problem as a system of integro-differential equations defined solely on the microbial domain. From this formulation, we identify an axisymmetric solution corresponding to a radially expanding disk and analyze its morphological stability. We find that growth forces stabilize the axisymmetric solution while buoyancy forces destabilize it. We connect these findings to experimental observations.

Lilian Terezinha Costa, Lilian Terezinha Costa

David M. Johnson, Francis J. Nge, Gregory Stull et al.

Pantropical taxa with broad and changing distributions provide useful models for assessing drivers of tropical tree biodiversity. Originating at the Eocene-Oligocene boundary, Xylopia is a vertebrate-dispersed woody plant genus with ca. 190 species evenly distributed across the Tropics. How did biogeographic and ecological transitions in this genus shape its broad present-day distribution? We analysed these transitions using ancestral area, climatic and spatial phylogenetic reconstructions, based on an extensive nuclear phylogeny and a curated dataset of occurrence records. The ancestral area was reconstructed as palaeotropical. The genus then underwent two dispersals from Africa, one to the Asia-Pacific area and one to the Neotropics. While niche conservatism in continental rain forests continued, the genus repeatedly transitioned to subhumid, inundated and ultramafic environments. Transitions from rain forests to subhumid environments increased in the Afrotropics as many rain forest groups underwent extinction. Association with inundated habitats, frequent in the early evolution of the genus, became sporadic. Ultramafic transitions occurred in five clades. Xylopia is present on 51 tropical islands; single-island endemics make up ca. 90% of insular species. Repeated dispersals took place between Africa and Madagascar, the Sunda and Sahul plates in the Asia-Pacific and from Central America to the Caribbean. Island distributions indicate overdispersion to remote islands, as well as limited radiations and stepping-stone dispersals. Novel environments, including islands, acted largely as sinks, together encompassing about half the species in the genus. A suite of traits promoting long-distance dispersal by a variety of non-resident birds, combined with the capacity for habitat transitions, were fundamental drivers of pantropical expansion and diversification. These drivers operated repeatedly in all regions, while idiosyncratic historical factors determined the timing and routes of dispersals. Highlights Age and distribution of basal grade lineages suggest that the ancestral Xylopia lineage occupied Eocene Boreotropical forests, moving southwards and diversifying independently in the Afrotropic and Asia-Pacific areas of the Palaeotropics. Biogeographic stochastic mapping estimated high regional in situ speciation (89.8%) amongst total biogeographic events for Xylopia. The plants provide high value seed rewards taken by birds that transit long distances and between habitats, promoting long-distance dispersal. Xylopia exhibits overdispersion even to isolated islands, but there is no significant correlation between species richness and isolation index. In response to Miocene aridification and shifts to monsoon climates in the Afrotropics, Xylopia dispersed across multiple lineages, including transitions to subhumid habitats. Ultramafic species occur on islands throughout the range of Xylopia; radiations took place in Xylopia sect. Xylopia on Cuba and in Xylopia sect. Stenoxylopia on New Guinea and New Caledonia.

Kent H. Redford, Jack A. Gilbert, Raquel S. Peixoto

Chunlin Wang, Fan Chen, Jingjing Wang et al.

Efficient removal and recovery of uranium from mining wastewater are essential for environmental protection and resource sustainability. Microbial reduction of soluble U(VI) to insoluble U(IV) is a promising strategy, but the role of biostimulation via tailored carbon sources and electrochemical inputs remains underexplored. This study investigated how carbon sources and electrode stimulation affect U(VI) reduction efficiency, product formation, microbial communities, and metabolic functions. U(VI) removal followed the order of carbon source: glucose > lactic acid > sodium acetate. Electro-stimulation markedly enhanced U(VI) reduction, especially under sodium acetate conditions with E24h increased from 65.0% to 90.7% at 0.7 V, by promoting carbon sources utilization and accelerating the removal of competitive anions. Glucose and lactic acid promoted the formation of UO2, while sodium acetate favored U3O8. Electro-stimulation facilitated the formation of compact uranium precipitates, enhancing recovery potential and minimizing reoxidation risk. Electrochemical analyses revealed that glucose and lactic acid exhibited superior electrochemical behavior compared to sodium acetate. Combined biostimulation enriched redox-active, electroactive, and EPS-secreting microbial taxa, along with functional genes related to U(VI) reduction, electron transfer, and carbon metabolism. Glucose and lactic acid imposed stronger selection on microbial and genetic structures than sodium acetate. Electro-stimulation promoted metabolic diversification, enhancing microbial resilience and functional redundancy. This study offers valuable insights into electrochemical enhancement of the biological treatment of uranium-bearing wastewater.

Tianyi Dong, Qi Wang, Tengcheng Que et al.

Abstract Background Pangolins, the world’s most trafficked mammals, have emerged as critical subjects of study due to their potential role as intermediate hosts for zoonotic viruses. While previous studies have primarily focused on diseased pangolins, the virome composition of healthy individuals remains largely unexplored. Results To address this knowledge gap, we performed comprehensive metatranscriptomic analysis of 83 healthy pangolins, in comparison with virome data of 52 diseased individuals derived from previously published datasets. We identified 51 viral operational taxonomic units (vOTUs) across six mammalian-associated viral families: Parvoviridae, Picornaviridae, Papillomaviridae, Circoviridae, Flaviviridae, and Paramyxoviridae. Notably, we observed recombination in Morbillivirus canis isolate BJ16B35, Canine distemper virus strain PS, and UN_MBA191024-Paramyxoviridae-1 from pangolins and domestic dogs, suggesting cross-species transmission dynamics. Co-infection analysis revealed a strong positive correlation between Copiparvovirus P171T/pangolin/2018 and Pangolin protoparvovirus, suggesting possible shared transmission pathways. Several viruses, including Orthopneumovirus hominis and Orthorubulavirus mammalis, were exclusively detected in diseased pangolins, implicating their potential role in pathogenesis. Zoonotic risk assessment identified 16 vOTUs with high predicted potential for human infection, including Pangolin pestivirus and Manis javanica papillomavirus 1. Conclusions Our findings significantly expand our understanding of viral diversity in healthy pangolins and help distinguish commensal viral communities from potentially pathogenic ones. This research underscores the importance of continued wildlife viral surveillance for both conservation and public health preparedness. Video Abstract

Sukran Ozturk, F Gülden Ekmen, Hamza Ekmen et al.

This study, which bridges the disciplines of archaeology and microbiology, examines the ancient bacterial communities and antibiotic-resistance genes in soil samples collected from İnönü Cave in Zonguldak, Turkiye. Our aim is to provide a comprehensive understanding of historical human activities and their influence on microbial communities. Soil samples were gathered from four distinct cultural levels from the Chalcolithic Age to the Early Iron Age. The microbial communities were characterized, and antibiotic-resistance genes were identified using high-throughput sequencing of 16S rRNA genes and metagenomic studies. This interdisciplinary approach not only enriches our understanding of ancient microbial communities but also opens up new avenues for research and collaboration. The results of our study showed a wide range of microorganisms, including prominent bacterial groups such as Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, Cyanobacteria, Firmicutes, Myxococcota, and Proteobacteria. The study identified the presence of the tetracycline resistance gene tetA in Chalcolithic samples, the class 1 integron intl1 in Early Bronze Age samples, and the oxacillinase gene OXA58 in Late Bronze Age samples. These findings underscore the long-term impact of human activities on microbial communities, as antibiotic-resistance genes have been present and have remained over various historical periods, perhaps influenced by both human activities and environmental variables. This knowledge is crucial for understanding the resilience and adaptability of microbial communities in the face of human-induced changes. The coexistence of these resistance genes and alterations in the microbial population suggest substantial connections between human activities and soil microbiota. This study, which draws on the fields of archaeology, microbiology, and environmental science, offers valuable insights into the ancient microbial ecology and underscores the enduring presence of antibiotic resistance. It emphasizes the necessity of a comprehensive, interdisciplinary approach, spanning multiple fields, to comprehend microbial communities' evolution and resistance mechanisms in archaeological settings.

Johannes Nauta, Kaitlin A. Schaal, Ying-Jie Wang et al.

Microbiomes are complex systems comprised of many interacting species. Species can survive harsh or changing conditions by rapid adaptation, a process accelerated by the exchange of genetic material between different species through horizontal gene transfer. Conjugative plasmids are ubiquitous mobile genetic elements that mediate such exchanges both within and between species. Therefore, predicting whether a plasmid can invade and be maintained by a microbial community is critical, for example when assessing the risks of antimicrobial resistance gene spread in commensal or environmental microbiomes. However, existing theory developed to assist such predictions has generally focused on the balance among plasmid costs, benefits, and infection rates, overlooking other relevant factors such as the inherent dynamics and diversity of microbiomes. Here, we hypothesize that plasmid persistence in the absence of positive selection can arise purely from the heterogeneity present in large and diverse microbial communities. We introduce a generic model that integrates population-level dynamics with plasmid conjugation. Using this model, we show that we can predict plasmid maintenance, and that the probability for a plasmid to be maintained depends on traits of the plasmid, most importantly the conjugation rate, and the species abundance distribution of the community. Then, using both empirical abundance data and extensive numerical simulations, we demonstrate that the inherent randomness of ecological interactions and conjugation rates enables plasmid persistence -- even in the absence of positive selection. Our findings thus suggest that natural microbial communities are likely to maintain plasmids indefinitely, offering a new perspective on the spread, maintenance, and ubiquity of plasmids.

Daan R. Speth, Nick Pullen, Samuel T. N. Aroney et al.

Over the past years, substantial numbers of microbial species' genomes have been deposited outside of conventional INSDC databases. The GlobDB aggregates 14 independent genomic catalogues to provide a comprehensive database of species-dereplicated microbial genomes, with consistent taxonomy, annotations, and additional analysis resources. The GlobDB is available at https://globdb.org/.

Kyle Mason-Jones, S. Robinson, Ciska Veen et al.

Xia Xiao, Yixuan Zhou, Xinwei Li et al.

Abstract Background Gut microbiome metabolites are important modulators of host health and disease. However, the overall metabolic potential of the gut microbiome and interactions with the host organs have been underexplored. Results Using stable isotope resolved metabolomics (SIRM) in mice orally gavaged with 13C-inulin (a tracer), we first observed dynamic enrichment of 13C-metabolites in cecum contents in the amino acids and short-chain fatty acid metabolism pathways. 13C labeled metabolites were subsequently profiled comparatively in plasma, liver, brain, and skeletal muscle collected at 6, 12, and 24 h after the tracer administration. Organ-specific and time-dependent 13C metabolite enrichments were observed. Carbons from the gut microbiome were preferably incorporated into choline metabolism and the glutamine-glutamate/GABA cycle in the liver and brain, respectively. A sex difference in 13C-lactate enrichment was observed in skeletal muscle, which highlights the sex effect on the interplay between gut microbiome and host organs. Choline was identified as an interorgan metabolite derived from the gut microbiome and fed the lipogenesis of phosphatidylcholine and lysophosphatidylcholine in host organs. In vitro and in silico studies revealed the de novo synthesis of choline in the human gut microbiome via the ethanolamine pathway, and Enterococcus faecalis was identified as a major choline synthesis species. These results revealed a previously underappreciated role for gut microorganisms in choline biosynthesis. Conclusions Multicompartmental SIRM analyses provided new insights into the current understanding of dynamic interorgan metabolite transport between the gut microbiome and host at the whole-body level in mice. Moreover, this study singled out microbiota-derived metabolites that are potentially involved in the gut-liver, gut-brain, and gut-skeletal muscle axes. Video Abstract