Complex Communities Research Articles

Advancing Anti-Biofilm Strategies: Innovations to Combat Biofilm-Related Challenges and Enhance Efficacy.

Biofilms are complex communities of microorganisms that can cause significant challenges in various settings, including industrial processes, environmental systems, and human health. The protective nature of biofilms makes them resistant to traditional anti-biofilm strategies, such as chemical agents, mechanical interventions, and surface modifications. To address the limitations of conventional anti-biofilm methods, researchers have explored emerging strategies that encompass the use of natural compounds, nanotechnology-based methods, quorum-sensing inhibition, enzymatic degradation, and antimicrobial photodynamic/sonodynamic therapy. There is an increasing focus on combining multiple anti-biofilm strategies to combat resistance and enhance effectiveness. Researchers are continuously investigating the mechanisms of biofilm formation and developing innovative approaches to overcome the limitations of conventional anti-biofilm methods. These efforts aim to improve the management of biofilms and prevent infections while preserving the environment. This study provides a comprehensive overview of the latest advancements in anti-biofilm strategies. Given the dynamic nature of this field, exploring new approaches is essential to stimulate further research and development initiatives. The effective management of biofilms is crucial for maintaining the health of industrial processes, environmental systems, and human populations.

Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology.

The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind and Earth. To that end, EEB is developing new transdisciplinary tools to analyze these ecologically critical, complex microbial communities. The American Society for Microbiology's Council on Microbial Sciences hosted a virtual retreat in 2023 to discuss the trajectory of EEB both within the Society and microbiology writ large. The retreat emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The maximal potential impact of EEB will not be achieved without contributions from disparate fields that unite diverse technologies and data sets. In turn, this level of transdisciplinary efforts requires actively encouraging "broad" research, spanning inclusive global collaborations that incorporate both scientists and the public. Together, the American Society for Microbiology and EEB are poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.

Compendium of Bifidobacterium-based probiotics: characteristics and therapeutic impact on human diseases

The human microbiota, a complex community of microorganisms residing in and on the human body, plays a crucial role in maintaining health and preventing disease. Bifidobacterium species have shown remarkable therapeutic potential across a range of health conditions, thus being considered optimal probiotic bacteria. This review provides insights into the concept of probiotics and explores the impact of bifidobacteria on human health, focusing on the gastrointestinal, respiratory, skeletal, muscular, and nervous systems. It also integrates information on the available genetic bases underlying the beneficial effects of each bifidobacterial probiotic species on different aspects of human physiology. Notably, Bifidobacterium -based probiotics have proven effective in managing gastrointestinal conditions such as constipation, antibiotic-associated diarrhea, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and Helicobacter pylori infections. These benefits are achieved by modulating the intestinal microbiota, boosting immune responses, and strengthening the gut barrier. Moreover, Bifidobacterium species have been reported to reduce respiratory infections and asthma severity. Additionally, these probiotic bacteria offer benefits for skeletal and muscular health, as evidenced by Bifidobacterium adolescentis and Bifidobacterium breve , which have shown anti-inflammatory effects and symptom relief in arthritis models, suggesting potential in treating conditions like rheumatoid arthritis. Furthermore, probiotic therapies based on bifidobacterial species have shown promising effects in alleviating anxiety and depression, reducing stress, and enhancing cognitive function. Overall, this review integrates the extensive scientific literature now available that supports the health-promoting applications of probiotic Bifidobacterium species and underscores the need for further research to confirm their clinical efficacy across different body systems.

Bacteriophage-mediated approaches for biofilm control.

Biofilms are complex microbial communities in which planktonic and dormant bacteria are enveloped in extracellular polymeric substances (EPS) such as exopolysaccharides, proteins, lipids, and DNA. These multicellular structures present resistance to conventional antimicrobial treatments, including antibiotics. The formation of biofilms raises considerable concern in healthcare settings, biofilms can exacerbate infections in patients and compromise the integrity of medical devices employed during treatment. Similarly, certain bacterial species contribute to bulking, foaming, and biofilm development in water environments such as wastewater treatment plants, water reservoirs, and aquaculture facilities. Additionally, food production facilities provide ideal conditions for establishing bacterial biofilms, which can serve as reservoirs for foodborne pathogens. Efforts to combat antibiotic resistance involve exploring various strategies, including bacteriophage therapy. Research has been conducted on the effects of phages and their individual proteins to assess their potential for biofilm removal. However, challenges persist, prompting the examination of refined approaches such as drug-phage combination therapies, phage cocktails, and genetically modified phages for clinical applications. This review aims to highlight the progress regarding bacteriophage-based approaches for biofilm eradication in different settings.

Microbiota of Attine Ants' Gardens: Visualizing a Microbial Landscape by Scanning Electron Microscopy.

In macroscale ecosystems, such as rainforests or coral reefs, the spatial localization of organisms is the basis of our understanding of community ecology. In the microbial world, likewise, microscale ecosystems are far from a random and homogeneous mixture of organisms and habitats. Accessing the spatial distribution of microbes is fundamental for understanding the functioning and ecology of the microbiota, as cohabiting species are more likely to interact and influence each other's physiology. An interkingdom microbial ecosystem is at the core of fungus-growing ant colonies, which cultivate basidiomycete fungi as a nutritional resource. Attine ants forage for diverse substrates (mostly plant-based), metabolized by the cultivated fungus while forming a spongy structure, a "microbial garden" that acts as an external gut. The garden is an intertwined mesh of fungal hyphae growing by metabolizing the substrate, opening niches for a characteristic and adapted microbiota to establish. The microbiota is thought to be a contributor to substrate degradation and fungal growth, though its spatial organization is yet to be determined. Here, we describe how we employ Scanning Electron Microscopy (SEM) to investigate, with unprecedented detail, the microbiota and biofilm spatial organization across different fungiculture systems of fungus-growing ants. SEM imaging has provided a description of the microbiota spatial structure and organization. SEM revealed that microbiota commonly assemble in biofilms, a widespread structure of the microbial landscapes in fungiculture. We present the protocols employed to fix, dehydrate, dry, sputter coating, and image such a complex community. These protocols were optimized to deal with delicate and heterogeneous samples, comprising plant and fungal biomass, as well as the microbiota and the biofilm.

Cyclic di-GMP as an antitoxin regulates bacterial genome stability and antibiotic persistence in biofilms.

Biofilms are complex bacterial communities characterized by a high persister prevalence, which contributes to chronic and relapsing infections. Historically, persister formation in biofilms has been linked to constraints imposed by their dense structures. However, we observed an elevated persister frequency accompanying the stage of cell adhesion, marking the onset of biofilm development. Subsequent mechanistic studies uncovered a comparable type of toxin-antitoxin (TA) module (TA-like system) triggered by cell adhesion, which is responsible for this elevation. In this module, the toxin HipH acts as a genotoxic deoxyribonuclease, inducing DNA double strand breaks and genome instability. While the second messenger c-di-GMP functions as the antitoxin, exerting control over HipH expression and activity. The dynamic interplay between c-di-GMP and HipH levels emerges as a crucial determinant governing genome stability and persister generation within biofilms. These findings unveil a unique TA system, where small molecules act as the antitoxin, outlining a biofilm-specific molecular mechanism influencing genome stability and antibiotic persistence, with potential implications for treating biofilm infections.

Rescue of morphological defects in Streptomyces venezuelae by the alkaline volatile compound trimethylamine.

Bacterial volatiles have a wide range of biological roles at intra- or inter-kingdom levels. The impact of volatiles has mainly been observed between producing bacteria and recipient bacteria, mostly of different species. In this study, we report that the wild-type, soil-dwelling bacterium Streptomyces venezuelae, which forms aerial hypha and spores as part of its normal developmental cycle, also produces the alkaline volatile compound trimethylamine (TMA) under multiple growth conditions. We showed that the environmental dispersion of TMA produced by S. venezuelae promotes the growth and differentiation of growth-deficient mutants of the same species or other slowly growing Streptomyces bacteria, and thus aids in their survival and their ability to compete in complex environmental communities such as soil. Our novel findings suggest a potentially profound biological role for volatile compounds in the growth and survival of communities of volatile-producing Streptomyces species.

Selection for amoxicillin-, doxycycline-, and enrofloxacin-resistant Escherichia coli at concentrations lower than the ECOFF in broiler-derived cecal fermentations.

Antimicrobial resistance (AMR) is an emerging worldwide problem and a health threat for humans and animals. Antimicrobial usage in human and animal medicine or in agriculture results in selection for AMR. The selective concentration of antimicrobial compounds can be lower than the minimum inhibitory concentration and differs between environments, which can be a reason for bacterial resistance. Therefore, knowledge of the minimal selective concentration (MSC), under natural conditions, is essential to understand the selective window of bacteria when exposed to residual antimicrobials. In this study, we estimated the MSCs of three antimicrobials, amoxicillin, doxycycline, and enrofloxacin in a complex microbial community by conducting fermentation assays with cecal material derived from broilers. We examined the phenotypic resistance of Escherichia coli, resistome, and microbiome after 6 and 30 hours of fermenting in the presence of the antimicrobials of interest. The concentrations were estimated to be 10-100 times lower than the epidemiological cut-off values in E. coli for the respective antimicrobials as determined by EUCAST, resulting in an MSC between 0.08 and 0.8 mg/L for amoxicillin, 0.4 and 4 mg/L for doxycycline, and 0.0125 and 0.125 mg/L for enrofloxacin. Additionally, resistome analysis provided an MSC for doxycycline between 0.4 and 4 mg/L, but amoxicillin and enrofloxacin exposure did not induce a significant difference. Our findings indicate at which concentrations there is still selection for antimicrobial-resistant bacteria. This knowledge can be used to manage the risk of the emergence of antimicrobial-resistant bacteria.IMPORTANCEAntimicrobial resistance possibly affects human and animal health, as well as economic prosperity in the future. The rise of antimicrobial-resistant bacteria is a consequence of using antimicrobial compounds in humans and animals selecting for antimicrobial-resistant bacteria. Concentrations reached during treatment are known to be selective for resistant bacteria. However, at which concentrations residues are still selective is important, especially for antimicrobial compounds that remain in the environment at low concentrations. The data in this paper might inform decisions regarding guidelines and regulations for the use of specific antimicrobials. In this study, we are providing these minimal selective concentrations for amoxicillin, doxycycline, and enrofloxacin in complex environments.

Role of TM7 in the Oral Microbiome and its Implications for Periodontal Disease: A Systematic Review

ABSTRACT Periodontal disease, a prevalent oral health condition, involves a complex microbial community. Advanced sequencing technologies have enabled in-depth studies of the oral microbiome, focusing on specific bacterial taxa like TM7. This systematic review analyzes the role of TM7 in the oral microbiome and its implications for periodontal disease. This review underscores TM7’s importance in the oral microbiome and its potential as a target for future research on periodontal disease pathogenesis.

Carlos Asensio and the dawn of molecular microbial ecology.

At near 50years of the discovery of microcins, this article highlights the pivotal-but under-recognised-influence of Spanish biochemist Carlos Asensio (1925-1982) in contemporary microbiology, featuring the epistemological, sociological, and cultural impact of his scientific achievements. At a time when the intestinal microbiome is central to current biomedical research, it is due to emphasise his role in the establishment of new scientific fields that are now considered fundamental. Despite his premature death at the peak of his conceptual and experimental creativity, many of his ideas about microbial communication in complex communities inspired a generation of researchers and opened new topics reach to this day. Asensio was also a trailblazer in Spain, advocating for fundamental research within the socio-economic context of his time. He foresaw the shift towards what is now termed the knowledge-based bioeconomy, recognised the need for multidisciplinary research teams, and advocated integration science into societal and political agendas. These facets became evident during his research on microcins, low molecular weight bioactive compounds produced by enterobacteria. These molecules were hypothesised as mediators of microbial interactions in the human gut and were considered potential new antibiotics and even antitumoral agents. His research mobilised young talent and attracted unprecedented resources in Spain during the late 1970s-early 1980s. It underscored the medical value of microbial ecology and exemplified the benefits of collaboration between academia and industry. Asensio played a pivotal role in the emergence of molecular microbial ecology as a research discipline and its foundational and applied significance in biotechnology.

Classifying compounds as prebiotics - scientific perspectives and recommendations.

Microbiomes provide key contributions to health and potentially important therapeutic targets. Conceived nearly 30 years ago, the prebiotic concept posits that targeted modulation of host microbial communities through the provision of selectively utilized growth substrates provides an effective approach to improving health. Although the basic tenets of this concept remain the same, it is timely to address certain challenges pertaining to prebiotics, including establishing that prebiotic-induced microbiota modulation causes the health outcome, determining which members within a complex microbial community directly utilize specific substrates in vivo and when those microbial effects sufficiently satisfy selectivity requirements, and clarification of the scientific principles on which the term 'prebiotic' is predicated to inspire proper use. In this Expert Recommendation, we provide a framework for the classification of compounds as prebiotics. We discuss ecological principles by which substrates modulate microbiomes and methodologies useful for characterizing such changes. We then propose statistical approaches that can be used to establish causal links between selective effects on the microbiome and health effects on the host, which can help address existing challenges. We use this information to provide the minimum criteria needed to classify compounds as prebiotics. Furthermore, communications to consumers and regulatory approaches to prebiotics worldwide are discussed.

Mechanism of carbonized humic acid and magnesium aluminum-layered double hydroxide promoting biohydrogen generation

Dark fermentation (DF) is prone to low hydrogen (H2) yield. In this work, magnesium aluminum-layered double hydroxide and carbonized humic acid (MgAl-LDH/CHA) was synthesized by co-precipitation to reveal the mechanism in rising bioH2 generation. The results indicated that MgAl-LDH released Mg and Al ions slowly in DF system, improving the activity of H2-producing microbes (HPM) for more H2. The H2 yield increased from 169.3 mL/g glucose to 244.9 mL/g glucose, which was 44.7 % higher than that for the control yield. MgAl-LDH/CHA increased Proteobacteria content from 30.9 % to 43.7 %, making it form a complex microbial community and participate in DF metabolism with Firmicutes and other microbes together. Besides, MgAl-LDH/CHA could serve as an electron shuttle that likely effectively promotes electron transfer in DF, significantly reduced the energy requirements of HPM, thus raising metabolic activity. It provides direction for the multi-element composite applied in DF system.

Synergistic biodegradation of trichloroethylene-contaminated soil using Typha angustifolia L. and an anaerobic degrading bacterial consortium

Plant-microorganism combined bioremediation is a highly efficient and environmentally sustainable method for the remediation of contaminated soils. Despite its potential, the synergistic effects of wetland plants and anaerobic microbial consortium on the removal of chlorinated hydrocarbons (CAHs) from soil remain inadequately understood. In this study, an anaerobic bacterial consortium, capable of completely dechlorinating trichloroethylene (TCE), was enriched and screened from long-term CAH-contaminated soil. Subsequently, the combined effects of the wetland plant Typha angustifolia L. and the degrading bacterial consortium on the removal of TCE from soil were investigated, along with the underlying microbial mechanisms. The results demonstrated that the bacterial consortium was able to completely convert 0.5 mM TCE to vinyl chloride (VC) within 7 days, and subsequently degrade VC to ethylene within 48 days. The integration of Typha angustifolia L. with the degrading bacterial consortium significantly enhanced both the removal and complete dechlorination of TCE from the soil compared to either treatment alone. Furthermore, this combination substantially increased the diversity and richness of soil bacterial communities, enriched dechlorinating microorganisms, and elevated the relative abundance of dehalogenating enzymes and peroxidases involved in pollutant degradation. In addition, the combination resulted in a more complex soil bacterial community, closer microbial interactions, and a more stable microbial co-occurrence network. This study extends the scope of plant-microorganism combined bioremediation for CAH- contaminated soils.

Bacterial Community Structure Modulates Soil Phosphorus Turnover at Early Stages of Primary Succession

AbstractMicrobes are the drivers of soil phosphorus (P) cycling in terrestrial ecosystems; however, the role of soil microbes in mediating P cycling in P‐rich soils during primary succession remains uncertain. This study examined the impacts of bacterial community structure (diversity and composition) and its functional potential (absolute abundances of P‐cycling functional genes) on soil P cycling along a 130‐year glacial chronosequence on the eastern Tibetan Plateau. Bacterial community structure was a better predictor of soil P fractions than P‐cycling genes along the chronosequence. After glacier retreat, the solubilization of inorganic P and the mineralization of organic P were significantly enhanced by increased bacterial diversity, changed interspecific interactions, and abundant species involved in soil P mineralization, thereby increasing P availability. Although 84% of P‐cycling genes were associated with organic P mineralization, these genes were more closely associated with soil organic carbon than with organic P. Bacterial carbon demand probably determined soil P turnover, indicating the dominant role of organic matter decomposition processes in P‐rich alpine soils. Moreover, the significant decrease in the complexity of the bacterial co‐occurrence network and the taxa‐gene‐P network at the later stage indicates a declining dominance of the bacterial community in driving soil P cycling with succession. Our results reveal that bacteria with a complex community structure have a prominent potential for biogeochemical P cycling in P‐rich soils during the early stages of primary succession.

Healthcare system navigation difficulties among informal caregivers of older adults: a logistic regression analysis of social capital, caregiving support and utilization factors

BackgroundInformal caregivers of older adults play a vital role in improving the degree to which older adults access community and healthcare services in a seamless and timely manner. They are fulfilling important navigation and support roles for their older care recipients. However, there is still little knowledge of the most significant facilitators and barriers to effective and efficient system navigation among caregivers. This paper aims to fill these knowledge gaps through investigation of the key factors (i.e., social capital/cohesion, caregiving supports, and utilization factors) affecting navigation difficulties faced by informal caregivers of older adults.MethodsThe Behavioural-Ecological Framework of Healthcare Access and Navigation (BEAN) model is used to frame the study. Using the General Social Survey on Caregiving and Care Receiving 2018, we analyzed 2,733 informal caregivers whose primary care recipients were aged 65 or older. Hierarchical logistic regression was conducted to identify the relationship between system navigation difficulties among informal caregivers and four sequentially ordered blocks of predictors: (1) sociodemographic (2), social capital/cohesion (3), caregiving supports, and (4) healthcare demand.ResultsThe fully adjusted model showed that the probability of reporting navigation difficulties was lower for caregivers with social capital/cohesion compared to those without social capital/cohesion. In comparison, the probability of reporting navigation difficulties was higher among caregivers with caregiving support and among caregivers whose care receivers use a higher amount of health service use. Several sociodemographic covariates were also identified.ConclusionOur findings support certain aspects of the BEAN model. This study extends our understanding of potential facilitators and barriers that informal caregivers of older adults face while navigating complex community and health systems. There is a need to implement coordinated schemes and health policies especially for older adults with mental/neurological issues to address the challenges of their caregivers given the specific vulnerability identified in this study. The need for further research using different approaches to examine the disproportionate impact of COVID-19 on caregivers’ system navigation experience is crucial.

Microbial single-cell applications under anoxic conditions.

The field of microbiology traditionally focuses on studying microorganisms at the population level. Nevertheless, the application of single-cell level methods, including microfluidics and imaging techniques, has revealed heterogeneity within populations, making these methods essential to understand cellular activities and interactions at a higher resolution. Moreover, single-cell sorting has opened new avenues for isolating cells of interest from microbial populations or complex microbial communities. These isolated cells can be further interrogated in downstream single-cell "omics" analyses, providing physiological and functional information. However, applying these methods to study anaerobic microorganisms under in situ conditions remains challenging due to their sensitivity to oxygen. Here, we review the existing methodologies for the analysis of viable anaerobic microorganisms at the single-cell level, including live-imaging, cell sorting, and microfluidics (lab-on-chip) applications, and we address the challenges involved in their anoxic operation. Additionally, we discuss the development of non-destructive imaging techniques tailored for anaerobes, such as oxygen-independent fluorescent probes and alternative approaches.

Helechos y licofitas del Área Natural Protegida “Paisaje Protegido Cerro Mbororé” (Misiones, Argentina).

Background and aims: In this work, the ferns and lycophytes of the Paisaje Protegido Cerro Mbororé, Oberá, Misiones, Argentina are studied. The phytogeographic importance of the area is discussed, since it is located in the transition between the District of the Mixed Forests and the District of the Fields, in the Amazonian Domain from the country. M&M: The collected materials were deposited in the LP, BA, and SLP herbaria. For the identification of species, the Flora Argentina and local floras were used. The photographs taken in the field were uploaded to the iNarulatist platform. The herbarium specimens studied are mentioned in this section. Results: The study area has 32 species of ferns (nine families) and one species of lycophytes. The most diverse family is Pteridaceae, with six genera and 13 species, followed by Polypodiaceae, with three genera and four species. Four well-defined environments with particular associations of species are identified: the top of the hill, the high-altitude lagoon, the north slope and the south slope. Conclusions: The environmental heterogeneity, product of the steep relief, and the transitional position of the area, generate a complex community of ferns and lycophytes with an important environmental value, which must be protected from the danger of the advance of the agricultural frontier and forestry exploitation.

Time-To-Event Analysis Of Factors Influencing Delay In Discharge From A Subacute Complex Discharge Unit During The Pandemic

Abstract Background Length of stay (LOS) is the most common outcome measure of effectiveness in discharge planning. It refers to the time expressed in days between admission to and discharge from the hospital. During the COVID-19 pandemic, the average inpatient LOS was 5.8 days, representing a slight increase in the average inpatient LOS of 5.7 days between 2016–2019. Tackling delays in patient discharge is an ongoing challenge, and with the emergence of the COVID-19 pandemic, there has been significant disruptions in discharge planning, discontinuity and incoordination between subacute complex discharge units and community care. Methods Our study analysed delaying factors amongst patients with LOS > 15 days during the COVID-19 pandemic using time-to-event analysis. Kaplan–Meier’s plot compared factors causing a delay in discharge to the single factors: age, gender, and multimorbidity. A multivariate Cox regression analysis adjusted to age, gender, and multimorbidity predicted factors affecting LOS. Results A total of 390 patients were admitted between March 2020 – February 2021 to a subacute complex discharge unit in an Irish tertiary centre hospital: 326 (83.6%) were >65 years of age and 233 (59.7%) were female. The median (IQR) age was 79 (70–86) years with a median (IQR) of 19.4 (10–41) days. A total of 237 (60.7%) events were uncensored, with LOS > 15 days, of which 138 (58.2%) were female and 124 (52.32%) had > 4 comorbidities; 153 (39.2%) were censored into LOS ≤ 15 days, and death occurred in 19 (4.8%). Conclusion Our study is the first to analyse common factors delaying discharge from a complex discharge unit. Further research is required to explore multimorbidity as a risk factor for mortality in patients with prolonged LOS within a complex discharge unit and target gender-specific frailty measures to achieve high-quality patient management.

Research Progress on the Correlation between Gut Microorganisms and Gastrointestinal Diseases

The intestinal microbiota refers to the complex community of microorganisms present in the human digestive tract. With the development of high-throughput sequencing technologies such as 16SrRNA gene sequencing and metagenomic sequencing, the intestinal microbiota has been shown to be closely related to gastric cancer and colorectal cancer. At the same time, a series of studies have been conducted to explore the intestinal microbiota as a new type of non-invasive biological marker. This article summarizes the research on the intestinal microbiota of gastric cancer and colorectal cancer, and explains the changes in the intestinal microbiota when the disease occurs, so as to provide new ideas for finding potential molecular targets for the prevention, treatment, and intervention of tumors.

Gut Microbiota Mediates Neuroinflammation in Alzheimer's Disease: Unraveling Key Factors and Mechanistic Insights.

The gut microbiota, the complex community of microorganisms that inhabit the gastrointestinal tract, has emerged as a key player in the pathogenesis of neurodegenerative disorders, including Alzheimer's disease (AD). AD is characterized by progressive cognitive decline and neuronal loss, associated with the accumulation of amyloid-β plaques, neurofibrillary tangles, and neuroinflammation in the brain. Increasing evidence suggests that alterations in the composition and function of the gut microbiota, known as dysbiosis, may contribute to the development and progression of AD by modulating neuroinflammation, a chronic and maladaptive immune response in the central nervous system. This review aims to comprehensively analyze the current role of the gut microbiota in regulating neuroinflammation and glial cell function in AD. Its objective is to deepen our understanding of the pathogenesis of AD and to discuss the potential advantages and challenges of using gut microbiota modulation as a novel approach for the diagnosis, treatment, and prevention of AD.