Bacteria dominate the biosphere and assemble into highly diverse communities, yet the mechanisms by which these communities migrate remain poorly understood. Here, we used a meso-tube chemotaxis assay to track taxonomic, functional and genomic shifts within sewage-derived microbial communities that migrate in self-organized bands over metre scales. Chemotactic bands accelerated during migration and incorporated non-motile bacterial hitchhikers as well as up to 10⁶ viruses/mL. Approximately 500 species co-migrated, with relative abundances fluctuating by orders of magnitude over time. The final communities exhibited enrichment of functional genes linked to motility and chemotaxis, consistent with adaptation to migration. Despite this functional convergence, replicate communities differed in taxonomic composition, reflecting environmental filtering that selects for functionally equivalent species. By revealing how chemotaxis governs large-scale microbial migration, this work provides a framework for understanding microbial spread in natural ecosystems and host-associated environments.

Microplastics are pervasive environmental contaminants of increasing ecological concern. Despite substantial advances in analytical techniques, reliable microplastic detection remains challenging due to their small size, physicochemical heterogeneity, and close resemblance to natural particles. Additionally, many conventional detection techniques are inherently slow, low-throughput, or limited in their ability to detect the smallest and most environmentally relevant microplastics. Standard flow cytometry is emerging as a complementary approach for microplastic detection, offering rapid, high-throughput, multiparametric analysis with high sensitivity for identifying small particles. Imaging flow cytometry offers these capabilities while incorporating image acquisition to enable morphological characterisation and visual confirmation of microplastics. Despite this potential, the application of both techniques to environmental microplastic analysis remains relatively underexplored. This review provides a comprehensive evaluation of standard and imaging flow cytometry for environmental microplastic detection, examining stain-based and stain-free workflows and highlighting the complementary strengths of each approach. We critically compare the performance, advantages, limitations, and applications of both techniques alongside microscopy, spectroscopy, imaging, and thermo-analytical methods. Particular emphasis is placed on the environmental and methodological factors influencing detection and the remaining challenges associated with applying these techniques to environmental samples. Finally, emerging technologies, including machine learning, artificial intelligence, spectral flow cytometry, and hybrid analytical approaches, are discussed as future directions for improving the sensitivity, robustness, and broader environmental applicability of both techniques. Together, these developments have the potential to support the integration of standard and imaging flow cytometry into future environmental microplastic monitoring workflows.

Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent "Clusters of Phylogeny and Functions" (COPFs). Coupled with gradient-boosted random forests, COPFs predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant P. aeruginosa signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent Aspergillus fumigatus signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting P. aeruginosa status across platforms and geographies, validating the model's universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.

Pollution of natural ecosystems is a global concern, with industrialisation contaminating millions of soil and water sites. These contaminants threaten human health, agricultural productivity, and ecological balance. Traditional bioaugmentation strategies, while cost-effective and sustainable, face challenges including slow degradation rates and environmental constraints on microbial efficacy. This mini review examines phage bioaugmentation, which uses bacteriophages to enhance microbial pollutant degradation and support a circular economy. We focus on lysogenic phages that integrate auxiliary metabolic genes into bacterial hosts to improve degradation capacity, synthesise current knowledge, identify challenges, and propose a conceptual workflow for implementation.

Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region’s 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth’s most rapidly changing marine environments.

Complications of diabetes, such as diabetic foot ulcers (DFUs), are common, multifactorial in origin, and costly to treat. DFUs are the cause of nearly 90% of limb amputations among persons with diabetes. In most chronic infections such as DFU, biofilms are involved. Bacteria in biofilms are 100–1000 times more resistant to antibiotics than their planktonic counterparts. Multidrug-resistant (MDR) Staphylococcus aureus and Pseudomonas aeruginosa infections in DFUs may require alternative therapeutic agents such as bacteriophages ("phages"). This study describes the lytic activity of phage cocktails AB-SA01 (3-phage cocktail) and AB-PA01 (4-phage cocktail), which target S. aureus and P. aeruginosa, respectively. The host range and lytic effect of AB-SA01 and AB-PA01 on a planktonic culture, single-species biofilm, and mixed-species biofilm were evaluated. In vitro testing showed that 88.7% of S. aureus and 92.7% of P. aeruginosa isolates were susceptible to AB-SA01 and AB-PA01, respectively, in the planktonic state. The component phages of AB-SA01 and AB-PA01 infected 66% to 94.3% of the bacterial isolates tested. Furthermore, AB-SA01 and AB-PA01 treatment significantly (p < 0.05) reduced the biofilm biomass of their hosts, regardless of the antibiotic-resistant characteristics of the isolates and the presence of a non-susceptible host. In conclusion, the strong lytic activity, broad host range, and significant biofilm biomass reduction of AB-SA01 and AB-PA01 suggest the considerable potential of phages in treating antibiotic-resistant S. aureus and P. aeruginosa infections alone or as coinfections in DFUs.

Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters' contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude.

Flow cytometry is an established method for the detection and enumeration of viruses. However, the technique is unable to target specific viral species. Here, we present OligoFlow, a novel method for the rapid detection and enumeration of viruses by incorporating flow cytometry with species specific oligonucleotide hybridization. Using Ostried herpesvirus and dengue virus as model organisms, we demonstrate high-level detection and specificity. Our results represent a significant advancement in viral flow cytometry, opening the possibilities for the rapid identification of viruses in time critical settings.

Background Due to the ever-expanding gap between the number of proteins being discovered and their functional characterization, protein function inference remains a fundamental challenge in computational biology. Currently, known protein annotations are organized in human-curated ontologies, however, all possible protein functions may not be organized accurately. Meanwhile, recent advancements in natural language processing and machine learning have developed models which embed amino acid sequences as vectors in n-dimensional space. So far, these embeddings have primarily been used to classify protein sequences using manually constructed protein classification schemes. Results In this work, we describe the use of amino acid sequence embeddings as a systematic framework for studying protein ontologies. Using a sequence embedding, we show that the bacterial carbohydrate metabolism class within the SEED annotation system contains 48 clusters of embedded sequences despite this class containing 29 functional labels. Furthermore, by embedding Bacillus amino acid sequences with unknown functions, we show that these unknown sequences form clusters that are likely to have similar biological roles. Conclusions This study demonstrates that amino acid sequence embeddings may be a powerful tool for developing more robust ontologies for annotating protein sequence data. In addition, embeddings may be beneficial for clustering protein sequences with unknown functions and selecting optimal candidate proteins to characterize experimentally.

Environments shape communities by driving individual interactions and the evolutionary outcome of competition. In static, homogeneous environments a robust, evolutionary stable, outcome is sometimes reachable. However, inherently stochastic, this evolutionary process need not stabilize, resulting in a dynamic ecological state, often observed in microbial communities. We use evolutionary games to study the evolution of phenotypic competition in dynamic environments. Under the assumption that phenotypic expression depends on the environmental shifts, existing periodic relationships may break or result in formation of new periodicity in phenotypic interactions. The exact outcome depends on the environmental shift itself, indicating the importance of understanding how environments influence affected systems. Under periodic environmental fluctuations, a stable state preserving dominant phenotypes may exist. However, rapid environmental shifts can lead to critical shifts in the phenotypic evolutionary balance. This might lead to environmentally favoured phenotypes dominating making the system vulnerable. We suggest that understanding of the robustness of the system’s current state is necessary to anticipate when it will shift to a new equilibrium via understanding what level of perturbations the system can take before its equilibrium changes. Our results provide insights in how microbial communities can be steered to states where they are dominated by desired phenotypes.

The two most commonly used wine microorganisms, Saccharomyces cerevisiae yeast and Oenococcus oeni bacteria, are responsible for completion of alcoholic and malolactic fermentation (MLF), respectively. For successful co-inoculation, S. cerevisiae and O. oeni must be able to complete fermentation; however, this relies on compatibility between yeast and bacterial strains. For the first time, quantitative trait loci (QTL) analysis was used to elucidate whether S. cerevisiae genetic makeup can play a role in the ability of O. oeni to complete MLF. Assessment of 67 progeny from a hybrid S. cerevisiae strain (SBxGN), co-inoculated with a single O. oeni strain, SB3, revealed a major QTL linked to MLF completion by O. oeni. This QTL encompassed a well-known translocation, XV-t-XVI, that results in increased SSU1 expression and is functionally linked with numerous phenotypes including lag phase duration and sulphite export and production. A reciprocal hemizygosity assay was performed to elucidate the effect of the gene SSU1 in the SBxGN background. Our results revealed a strong effect of SSU1 haploinsufficiency on O. oeni’s ability to complete malolactic fermentation during co-inoculation and pave the way for the implementation of QTL mapping projects for deciphering the genetic bases of microbial interactions. • For the first time, QTL analysis has been used to study yeast-bacteria interactions. • A QTL encompassing a translocation, XV-t-XVI, was linked to MLF outcomes. • S. cerevisiae SSU1 haploinsufficiency positively impacted MLF by O. oeni.

A universal scaling relationship exists between organism abundance and body size[1][1],[2][2]. Within ocean habitats this relationship deviates from that generally observed in terrestrial systems[2][2]–[4][3], where marine macro-fauna display steeper size-abundance scaling than expected. This is indicative of a fundamental shift in food-web organization, yet a conclusive mechanism for this pattern has remained elusive. We demonstrate that while fishing has partially contributed to the reduced abundance of larger organisms, a larger effect comes from ocean turbulence: the energetic cost of movement within a turbulent environment induces additional biomass losses among the nekton. These results identify turbulence as a novel mechanism governing the marine size-abundance distribution, highlighting the complex interplay of biophysical forces that must be considered alongside anthropogenic impacts in processes governing marine ecosystems. ### Competing Interest Statement The authors have declared no competing interest. [1]: #ref-1 [2]: #ref-2 [3]: #ref-4

The ability of influenza A virus to evolve, coupled with increasing antimicrobial resistance, could trigger an influenza pandemic with great morbidity and mortality. Much of the 1918 influenza pandemic mortality was likely due to bacterial coinfection, including Staphylococcus aureus pneumonia. S. aureus resists many antibiotics. The lack of new antibiotics suggests alternative antimicrobials, such as bacteriophages, are needed. Potential delivery routes for bacteriophage therapy (BT) include inhalation and intravenous injection. BT has recently been used successfully in compassionate access pulmonary infection cases. Phage lysins, enzymes that hydrolyze bacterial cell walls and which are bactericidal, are efficacious in animal pneumonia models. Clinical trials will be needed to determine whether BT can ameliorate disease in influenza and S. aureus coinfection.

Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-Macarthur ODEs to eliminate prey-mass dependency. We define the functional response term to match experiments, and examine situations where metabolic theory derivations and observation diverge. We produce dynamics consistent with observation. Our parameterisation of the Rosenzweig-Macarthur system is an accurate minimal model across 15+ orders of mass magnitude.

Flow cytometry is a high-throughput tool for determining microbial abundance in a range of medical, environmental, and food-related samples. For wine, determining the abundance of Saccharomyces cerevisiae is well-defined and reliable. However, for the most common wine bacterium, Oenococcus oeni, using flow cytometry to determine cell concentration poses some challenges. O. oeni most often occurs in doublets or chains of varying lengths that can be greater than seven cells. This wine bacterium is also small, at 0.2-0.6 μm and may exhibit a range of morphologies including binary fission and aggregated complexes. This work demonstrates a straightforward approach to determining the suitability of flow cytometry for the chain-forming bacteria, O. oeni, and considerations when using flow cytometry for the enumeration of small microorganisms (<0.5 μm). © 2020 International Society for Advancement of Cytometry.

Identifying members of the aquatic microbial community and their biotic and abiotic interactions are the first step in developing inocula for bio-floc starters used as aquaculture fish-feed. This research aims to identify whether a freshwater river with urban input can be used as a source of potential bio-floc forming bacteria. To identify the bacteria, 16S rDNA sequencing was performed, to determine the taxonomy and flow cytometry was employed to enumerate bacterial abundance. To resolve the complex interactions among microbes, microbial interaction networks were produced at the family level. Actinobacteria was found to be the most abundant bacterial phylum followed by Proteobacteria, Acidobacteria, and Chloroflexi that suggested the river was in health condition. Microbial interaction networks revealed nutrients, particularly nitrate, nitrite, ammonia, and silica, are crucial in maintaining network interactions, suggesting that urban nutrient input likely shapes the riverine microbial community. The families Actinomycetales F-ACK-M1, Rickettsiaceae, Betaproteobacteria O-SBla14 and Anaerolineae O-GCA004 demonstrated greatest network centrality, each interacting with seven first-neighbor taxa, suggesting an importance in community structure. Acetobacteraceae and Chloroflexi F-Dolo23 also exhibited network centrality and were directly linked to nitrate and nitrite, suggesting they play key roles in nitrogen cycling. Propionibacterium (44.82%) was the most dominant genera found in the Murray River followed by Anaerococcus (2.94%), and Finegoldia (2.05%). Comparison of the bacterial community comprising bio-floc and those found in the River Murray revealed that seven bacterial phyla including Proteobacteria, Bacteriodetes, Cyanobacteria, Actinobacteria, Planctomycetes, Verrumibrobia, and Chloroflexi common to bio-floc contributed to 95.8% total relative abundance in the river. However, based on genera level, there were14 bacteria genera in the river that generally present in bio-floc forming bacteria identified across all river samples constituted 4.63%. The potential bio-floc forming bacteria found mainly in downstream of the river provided various functions in the bio-floc system including producing natural flocculants to form microorganisms aggregates, a source of potential probiotics and prebiotics, nitrite oxidation and denitrification process, and degradation of organic matters.

The efficacy of phages in multispecies infections has been poorly examined. The in vitro lytic efficacies of phage cocktails AB-SA01, AB-PA01, which target Staphylococcus aureus and Pseudomonas aeruginosa, respectively, and their combination against their hosts were evaluated in S. aureus and P. aeruginosa mixed-species planktonic and biofilm cultures. Green fluorescent protein (GFP)-labelled P. aeruginosa PAO1 and mCherry-labelled S. aureus KUB7 laboratory strains and clinical isolates were used as target bacteria. During real-time monitoring using fluorescence spectrophotometry, the density of mCherry S. aureus KUB7 and GFP P. aeruginosa PAO1 significantly decreased when treated by their respective phage cocktail, a mixture of phage cocktails, and gentamicin. The decrease in bacterial density measured by relative fluorescence strongly associated with the decline in bacterial cell counts. This microplate-based mixed-species culture treatment monitoring through spectrophotometry combine reproducibility, rapidity, and ease of management. It is amenable to high-throughput screening for phage cocktail efficacy evaluation. Each phage cocktail, the combination of the two phage cocktails, and tetracycline produced significant biofilm biomass reduction in mixed-species biofilms. This study result shows that these phage cocktails lyse their hosts in the presence of non-susceptible bacteria. These data support the use of phage cocktails therapy in infections with multiple bacterial species.

Uncovering the role of environmental factors and finding critical factors which harbor significant fractions in governing microbial communities remain key questions in coastal marine systems. To detect the interactions between environmental factors and distributions of virio- and bacterioplankton in trophic coastal areas, we used flow cytometry to investigate the abundance of virio- and bacterioplankton covering 31 stations in the Bohai Sea of China. Our results suggested that the average abundance of total virus (TV) in winter (∼2.29×108 particles/mL) was slightly lower than in summer (∼3.83×108 particles/mL). The mean total bacterial abundance (TB) was much lower in winter (∼2.54×107 particles/mL) than in summer (∼5.43×107 particles/mL). Correlation analysis via redundancy analysis (RDA) and network analysis among virioplankton, bacterioplankton and environmental factors revealed that the abundances of viral and bacterial subpopulations depend on environmental factors. In winter, only temperature significantly influenced the abundances of virio- and bacterioplankton. In summer, in addition to temperature, both salinity and nutrient (SiO2) had a remarkable impact on the distribution of virio- and bacterioplankton. Our results showed a clear seasonal and trophic pattern throughout the whole water system, which revealed that temperature and eutrophication may play crucial roles in microbial distribution pattern.

Background Diabetic foot ulcer (DFU) is a serious complication of diabetes mellitus. Antibiotic-resistantStaphylococcus aureusis frequently isolated from DFU infections. Bacteriophages (phages) represent an alternative or adjunct treatment to antibiotic therapy. Here we describe the efficacy of AB-SA01, a cocktail of threeS. aureus Myoviridaephages, made to current good manufacturing practice (cGMP) standards, and which has undergone two phase I clinical trials, in treatment of multidrug-resistant (MDR)S. aureusinfections. Results Wounds of saline-treated mice showed no healing, but expanded and became inflamed, ulcerated, and suppurating. In contrast, AB-SA01 treatment decreased the bacterial load with efficacy similar or superior to vancomycin treatment. At the end of the treatment period, there was a significant decrease (p < 0.001) in bacterial load and wound size in infected phage- and vancomycin-treated groups compared with infected saline-treated mice. In phage-treated mice, wound healing was seen similar to vancomycin treatment. No mortality was recorded associated with infections, and post-mortem examinations did not show any evident pathological lesions other than the skin wounds. No adverse effects related to the application of phages were observed. Conclusion Topical application of phage cocktail AB-SA01 is effective, as shown by bacterial load reduction and wound closure, in the treatment of diabetic wound infections caused by MDRS. aureus. Our results suggest that topical phage cocktail treatment may be effective in treating antibiotic-resistantS. aureusDFU infections.

The effect of the Yellow Sea Warm Current (YSWC) on virio- and bacterioplankton communities in the Bohai Sea is unknown. In this study, the composition and dynamic changes of virio- and bacterioplankton at the entrance of the Bohai Sea were measured to determine the influence of the YSWC on those communities and vice versa. In the Bohai Strait, there were east to west gradients of water chemistry and hydrology. The turbulent mixing between the deep north-western ‘warm’ current, which is 9°C, and the cold, nutrient-rich Bohai Sea water at 7–8°C appears to stimulate the abundance of both viruses and heterotrophic bacteria, with numbers at the junction of ‘warm’ and cold water being almost 10-fold greater than in the low-thermohaline areas, and peaking where the temperature is the highest. The average viral and bacterial abundances in the north-eastern area are much higher than in the south-western area. It proved that the YSWC entered the Bohai Sea with poor biomass and exited with rich biomass, which, in turn, enriches the Yellow Sea microbial loop. Our results showed the dramatic effect of temperature rise and increasing eutrophication on microbial abundance and marine microbial communities.