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Journal: NPJ biofilms and microbiomes


Bath toys pose an interesting link between flexible plastic materials, potable water, external microbial and nutrient contamination, and potentially vulnerable end-users. Here, we characterized biofilm communities inside 19 bath toys used under real conditions. In addition, some determinants for biofilm formation were assessed, using six identical bath toys under controlled conditions with either clean water prior to bathing or dirty water after bathing. All examined bath toys revealed notable biofilms on their inner surface, with average total bacterial numbers of 5.5 × 106 cells/cm2(clean water controls), 9.5 × 106 cells/cm2(real bath toys), and 7.3 × 107 cells/cm2(dirty water controls). Bacterial community compositions were diverse, showing many rare taxa in real bath toys and rather distinct communities in control bath toys, with a noticeable difference between clean and dirty water control biofilms. Fungi were identified in 58% of all real bath toys and in all dirty water control toys. Based on the comparison of clean water and dirty water control bath toys, we argue that bath toy biofilms are influenced by (1) the organic carbon leaching from the flexible plastic material, (2) the chemical and biological tap water quality, (3) additional nutrients from care products and human body fluids in the bath water, as well as, (4) additional bacteria from dirt and/or the end-users' microbiome. The present study gives a detailed characterization of bath toy biofilms and a better understanding of determinants for biofilm formation and development in systems comprising plastic materials in contact with potable water.

Concepts: Biofilm, Fungus, Drinking water, Plastic, Bacteria, Tap water


It is well appreciated that microbial metabolism of drugs can influence treatment efficacy. Microbial β-glucuronidases in the gut can reactivate the excreted, inactive metabolite of irinotecan, a first-line chemotherapeutic for metastatic colorectal cancer. Reactivation causes adverse drug responses, including severe diarrhea. However, a direct connection between irinotecan metabolism and the composition of an individual’s gut microbiota has not previously been made. Here, we report quantitative evidence of inter-individual variability in microbiome metabolism of the inactive metabolite of irinotecan to its active form. We identify a high turnover microbiota metabotype with potentially elevated risk for irinotecan-dependent adverse drug responses. We link the high turnover metabotype to unreported microbial β-glucuronidases; inhibiting these enzymes may decrease irinotecan-dependent adverse drug responses in targeted subsets of patients. In total, this study reveals metagenomic mining of the microbiome, combined with metabolomics, as a non-invasive approach to develop biomarkers for colorectal cancer treatment outcomes.

Concepts: Archaea, Diarrhea, Chemotherapy, Gut flora, Cancer, Colorectal cancer, Metabolism, Bacteria


Biofouling is a major problem caused by bacteria colonizing abiotic surfaces, such as medical devices. Biofilms are formed as the bacterial metabolism adapts to an attached growth state. We studied whether bacterial metabolism, hence biofilm formation, can be modulated in electrochemically active surfaces using the conducting conjugated polymer poly(3,4-ethylenedioxythiophene) (PEDOT). We fabricated composites of PEDOT doped with either heparin, dodecyl benzene sulfonate or chloride, and identified the fabrication parameters so that the electrochemical redox state is the main distinct factor influencing biofilm growth. PEDOT surfaces fitted into a custom-designed culturing device allowed for redox switching in Salmonella cultures, leading to oxidized or reduced electrodes. Similarly large biofilm growth was found on the oxidized anodes and on conventional polyester. In contrast, biofilm was significantly decreased (52-58%) on the reduced cathodes. Quantification of electrochromism in unswitched conducting polymer surfaces revealed a bacteria-driven electrochemical reduction of PEDOT. As a result, unswitched PEDOT acquired an analogous electrochemical state to the externally reduced cathode, explaining the similarly decreased biofilm growth on reduced cathodes and unswitched surfaces. Collectively, our findings reveal two opposing effects affecting biofilm formation. While the oxidized PEDOT anode constitutes a renewable electron sink that promotes biofilm growth, reduction of PEDOT by a power source or by bacteria largely suppresses biofilm formation. Modulating bacterial metabolism using the redox state of electroactive surfaces constitutes an unexplored method with applications spanning from antifouling coatings and microbial fuel cells to the study of the role of bacterial respiration during infection.

Concepts: Photosynthesis, Electrochemical cell, Cathode, Galvanic cell, Bacteria, Electrolysis, Redox, Electrochemistry


The biofilm chemical and physical properties in engineered systems play an important role in governing pathogen transmission, fouling facilities, and corroding metal surfaces. Here, we investigated how simulated drinking water biofilm chemical composition, structure, and stiffness responded to the common scale control practice of adjusting divalent ions and adding polyphosphate. Magnetomotive optical coherence elastography (MM-OCE), a tool developed for diagnosing diseased tissues, was used to determine biofilm stiffness in this study. MM-OCE, together with atomic force microscopy (AFM), revealed that the biofilms developed from a drinking water source with high divalent ions were stiffer compared to biofilms developed either from the drinking water source with low divalent ions or the water containing a scale inhibitor (a polyphosphate). The higher stiffness of biofilms developed from the water containing high divalent ions was attributed to the high content of calcium carbonate, suggested by biofilm composition examination. In addition, by examining the biofilm structure using optical coherence tomography (OCT), the highest biofilm thickness was found for biofilms developed from the water containing the polyphosphate. Compared to the stiff biofilms developed from the water containing high divalent ions, the soft and thick biofilms developed from the water containing polyphosphate will be expected to have higher detachment under drinking water flow. This study suggested that water chemistry could be used to predict the biofilm properties and subsequently design the microbial safety control strategies.


Mucus layers often provide a unique and multi-functional hydrogel interface between the epithelial cells of organisms and their external environment. Mucus has exceptional properties including elasticity, changeable rheology and an ability to self-repair by re-annealing, and is therefore an ideal medium for trapping and immobilising pathogens and serving as a barrier to microbial infection. The ability to produce a functional surface mucosa was an important evolutionary step, which evolved first in the Cnidaria, which includes corals, and the Ctenophora. This allowed the exclusion of non-commensal microbes and the subsequent development of the mucus-lined digestive cavity seen in higher metazoans. The fundamental architecture of the constituent glycoprotein mucins is also evolutionarily conserved. Although an understanding of the biochemical interactions between bacteria and the mucus layer are important to the goal of developing new antimicrobial strategies, they remain relatively poorly understood. This review summarises the physicochemical properties and evolutionary importance of mucus, which make it so successful in the prevention of bacterial infection. In addition, the strategies developed by bacteria to counteract the mucus layer are also explored.


Host-associated microbial communities play a fundamental role in the life of eukaryotic hosts. It is increasingly argued that hosts and their microbiota must be studied together as ‘holobionts’ to better understand the effects of environmental stressors on host functioning. Disruptions of host-microbiota interactions by environmental stressors can negatively affect host performance and survival. Substantial ecological impacts are likely when the affected hosts are habitat-forming species (e.g., trees, kelps) that underpin local biodiversity. In marine systems, coastal urbanisation via the addition of artificial structures is a major source of stress to habitat formers, but its effect on their associated microbial communities is unknown. We characterised kelp-associated microbial communities in two of the most common and abundant artificial structures in Sydney Harbour-pier-pilings and seawalls-and in neighbouring natural rocky reefs. The kelp Ecklonia radiata is the dominant habitat-forming species along 8000 km of the temperate Australian coast. Kelp-associated microbial communities on pilings differed significantly from those on seawalls and natural rocky reefs, possibly due to differences in abiotic (e.g., shade) and biotic (e.g., grazing) factors between habitats. Many bacteria that were more abundant on kelp on pilings belonged to taxa often associated with macroalgal diseases, including tissue bleaching in Ecklonia. There were, however, no differences in kelp photosynthetic capacity between habitats. The observed differences in microbial communities may have negative effects on the host by promoting fouling by macroorganisms or by causing and spreading disease over time. This study demonstrates that urbanisation can alter the microbiota of key habitat-forming species with potential ecological consequences.

Concepts: Ecklonia radiata, Kelp forest, Eukaryote, Microorganism, Archaea, Effect, Bacteria, Affect


Sequencing-based microbiome profiling aims at detecting and quantifying individual members of a microbial community in a culture-independent manner. While amplicon-based sequencing (ABS) of bacterial or fungal ribosomal DNA is the most widely used technology due to its low cost, it suffers from PCR amplification biases that hinder accurate representation of microbial population structures. Shotgun metagenomics (SMG) conversely allows unbiased microbiome profiling but requires high sequencing depth. Here we report the development of a meta-total RNA sequencing (MeTRS) method based on shotgun sequencing of total RNA and benchmark it on a human stool sample spiked in with known abundances of bacterial and fungal cells. MeTRS displayed the highest overall sensitivity and linearity for both bacteria and fungi, the greatest reproducibility compared to SMG and ABS, while requiring a ~20-fold lower sequencing depth than SMG. We therefore present MeTRS as a valuable alternative to existing technologies for large-scale profiling of complex microbiomes.

Concepts: Enzyme, Eukaryote, Fungus, DNA, Biotechnology, Microbiology, Bacteria, Molecular biology


Microbiomes of full-scale seawater reverse osmosis membranes are complex and subject to variation within and between membrane units. The pre-existing bacterial communities of unused membranes before operation have been largely ignored in biofouling studies. This study is novel as unused membranes were used as a critical benchmark for comparison. Fouled seawater reverse osmosis membrane biofilm communities from an array of autopsied membrane samples, following a 7-year operational life-span in a full-scale desalination plant in Western Australia, were characterised by 16S rRNA gene metabarcoding using the bacterial primers 515F and 806R. Communities were then compared based on fouling severity and sampling location. Microbiomes of proteobacterial predominance were detected on control unused membranes. However, fouled membrane communities differed significantly from those on unused membranes, reflecting that operational conditions select specific bacteria on the membrane surface. On fouled membranes, Proteobacteria were also predominant but families differed from those on unused membranes, followed by Bacteriodetes and Firmicutes. Betaproteobacteria correlated with stable, mature and thick biofilms such as those in severely fouled membranes or samples from the feed end of the membrane unit, while Alpha and Gammaproteobacteria were predominantly found in biofilms on fouled but visually clean, and moderately fouled samples or those from reject ends of membrane units. Gammaproteobacteria predominated the thin, compact biofilms at the mid-feed end of membrane units. The study also supported the importance of Caulobacterales and glycosphingolipid-producing bacteria, namely Sphingomonadales, Rhizobiales and Sphingobacteriia, in primary attachment and biofilm recalcitrance. Nitrate-and-nitrite-reducing bacteria such as Rhizobiales, Burkholderiales and some Pseudomonadales were also prevalent across all fouled membranes and appeared to be critical for ecological balance and biofilm maturation.

Concepts: Cell membrane, Ribosomal RNA, Microbiology, Archaea, 16S ribosomal RNA, Proteobacteria, Bacteria, Reverse osmosis


The emergence of drug-resistant pathogens has led to a decline in the efficacy of traditional antimicrobial therapy. The rise in resistance has been driven by widespread use, and in some cases misuse, of antibacterial agents in treating a variety of infections. A growing body of research has begun to elucidate the harmful effects of broad-spectrum antibiotic therapy on the beneficial host microbiota. To combat these threats, increasing effort is being directed toward the development of precision antimicrobial therapeutics that target key virulence determinants of specific pathogens while leaving the remainder of the host microbiota undisturbed. This includes the recent development of small molecules termed “mannosides” that specifically target uropathogenicE. coli(UPEC). Mannosides are glycomimetics of the natural mannosylated host receptor for type 1 pili, extracellular appendages that promotes UPEC colonization in the intestine. Type 1 pili are also critical for colonization and infection in the bladder. In both cases, mannosides act as molecular decoys which potently prevent bacteria from binding to host tissues. In mice, oral treatment with mannosides simultaneously clears active bladder infection and removes intestinal UPEC while leaving the gut microbiota structure relatively unchanged. Similar treatment strategies successfully target other pathogens, like adherent-invasiveE. coli(AIEC), an organism associated with Crohn’s disease (CD), in mouse models. While not without its challenges, antibiotic-sparing therapeutic approaches hold great promise in a variety of disease systems, including UTI, CD, otitis media (OM), and others. In this perspective we highlight the benefits, progress, and roadblocks to the development of precision antimicrobial therapeutics.

Concepts: Infectious disease, Ulcerative colitis, Therapy, Gut flora, Infection, Immune system, Microbiology, Bacteria


Colorectal cancer (CRC) remains the third most common cancer worldwide, with a growing incidence among young adults. Multiple studies have presented associations between the gut microbiome and CRC, suggesting a link with cancer risk. Although CRC microbiome studies continue to profile larger patient cohorts with increasingly economical and rapid DNA sequencing platforms, few common associations with CRC have been identified, in part due to limitations in taxonomic resolution and differences in analysis methodologies. Complementing these taxonomic studies is the newly recognized phenomenon that bacterial organization into biofilm structures in the mucus layer of the gut is a consistent feature of right-sided (proximal), but not left-sided (distal) colorectal cancer. In the present study, we performed 16S rRNA gene amplicon sequencing and biofilm quantification in a new cohort of patients from Malaysia, followed by a meta-analysis of eleven additional publicly available data sets on stool and tissue-based CRC microbiota using Resphera Insight, a high-resolution analytical tool for species-level characterization. Results from the Malaysian cohort and the expanded meta-analysis confirm that CRC tissues are enriched for invasive biofilms (particularly on right-sided tumors), a symbiont with capacity for tumorigenesis (Bacteroides fragilis), and oral pathogens including Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus stomatis. Considered in aggregate, species from the Human Oral Microbiome Database are highly enriched in CRC. Although no detected microbial feature was universally present, their substantial overlap and combined prevalence supports a role for the gut microbiota in a significant percentage (>80%) of CRC cases.

Concepts: Bacteroidetes, Microbiology, Ribosomal RNA, DNA, Archaea, 16S ribosomal RNA, Bacteria, Gut flora