Single particle tracking reveals spatial and dynamic organization of the Escherichia coli biofilm matrix

Biofilms are communities of surface-adherent bacteria surrounded by secreted polymers known as the extracellular polymeric substance. Biofilms are harmful in many industries, and thus it is of great interest to understand their mechanical properties and structure to determine ways to destabilize them. By performing single particle tracking with beads of varying surface functionalization it was found that charge interactions play a key role in mediating mobility within biofilms. With a combination of single particle tracking and microrheological concepts, it was found that Escherichia coli biofilms display height dependent charge density that evolves over time. Statistical analyses of bead trajectories and confocal microscopy showed inter-connecting micron scale channels that penetrate throughout the biofilm, which may be important for nutrient transfer through the system. This methodology provides significant insight into a particular biofilm system and can be applied to many others to provide comparisons of biofilm structure. The elucidation of structure provides evidence for the permeability of biofilms to microscale objects, and the ability of a biofilm to mature and change properties over time.National Science Foundation (U.S.) (CBET-1335938)Cystic Fibrosis Foundation (HANES07XX0)Massachusetts Institute of Technology (Charles E. Reed Faculty Initiative Fund)Burroughs Wellcome Fund (Preterm Birth Research Grant)National Institute of Allergy and Infectious Diseases (U.S.) (F30 Fellowship 1F30AI110053-01)National Institute of Allergy and Infectious Diseases (U.S.) (Training Grant in Toxicology 5 T32 ES7020-37

Mucins trigger dispersal of Pseudomonas aeruginosa biofilms

Mucus is a biological gel that lines all wet epithelia in the body, including the mouth, lungs, and digestive tract, and has evolved to protect the body from pathogenic infection. However, microbial pathogenesis is often studied in mucus-free environments that lack the geometric constraints and microbial interactions in physiological three-dimensional mucus gels. We developed fluid-flow and static test systems based on purified mucin polymers, the major gel-forming constituents of the mucus barrier, to understand how the mucus barrier influences bacterial virulence, particularly the integrity of Pseudomonas aeruginosa biofilms, which can become resistant to immune clearance and antimicrobial agents. We found that mucins separate the cells in P. aeruginosa biofilms and disperse them into suspension. Other viscous polymer solutions did not match the biofilm disruption caused by mucins, suggesting that mucin-specific properties mediate the phenomenon. Cellular dispersion depended on functional flagella, indicating a role for swimming motility. Taken together, our observations support a model in which host mucins are key players in the regulation of microbial virulence. These mucins should be considered in studies of mucosal pathogenesis and during the development of novel strategies to treat biofilms

Agriculture in the Karakum: An archaeobotanical analysis from Togolok 1, southern Turkmenistan (ca. 2300–1700 B.C.)

Southern Central Asia witnessed widespread expansion in urbanism and exchange, between roughly 2200 and 1500 B.C., fostering a new cultural florescence, sometimes referred to as the Greater Khorasan Civilization. Decades of detailed archeological investigation have focused on the development of urban settlements, political systems, and inter-regional exchange within and across the broader region, but little is known about the agricultural systems that supported these cultural changes. In this paper, we present the archaeobotanical results of material recovered from Togolok 1, a proto-urban settlement along the Murghab River alluvial fan located in southeastern Turkmenistan. This macrobotanical assemblage dates to the late 3rd - early 2nd millennia B.C., a time associated with important cultural transformations in southern Central Asia. We demonstrate that people at the site were cultivating and consuming a diverse range of crops including, barley, wheat, legumes, grapes, and possibly plums and apples or pears. This, together with the associated material culture and zooarchaeological evidence, suggest a regionally adapted mixed agropastoral economy. The findings at Togolok 1 contribute to the ongoing discussion of dietary choices, human/landscape interactions, and the adaptation of crops to diverse ecosystems in prehistoric Central Asia

Compounded Exclusion: Education for Disabled Refugees in Sub-Saharan Africa

International conventions acknowledge the right of refugees and of disabled people to access quality inclusive education. Both groups struggle to assert this right, particularly in the Global South, where educational access may be hindered by system constraints, resource limitations and negative attitudes. Our concern is the intersectional and compounding effect of being a disabled refugee in Sub-Saharan Africa. Disabled refugees have been invisible in policy and service provision, reliable data is very limited, and there has been little research into their experiences of educational inclusion and exclusion. This article makes the case for research to address this gap. Three country contexts (South Africa, Zimbabwe and Uganda) are presented to illustrate the multi-layered barriers and challenges to realizing the rights for disabled refugees in educational policy and practice. These three countries host refugees who have fled civil unrest and military conflict, economic collapse and natural disaster, and all have signed the United Nations Convention on the Rights of Persons with Disabilities. None has available and reliable data about the numbers of disabled refugees, and there is no published research about their access to education. Arguing for an inclusive and intersectional approach and for the importance of place and history, we illustrate the complexity of the challenge. This complexity demands conceptual resources that account for several iterative and mutually constituting factors that may enable or constrain access to education. These include legislation and policy, bureaucracy and resource capacity, schools and educational institutions, and community beliefs and attitudes. We conclude with a call for accurate data to inform policy and enable monitoring and evaluation. We advocate for the realization of the right to education for disabled refugee students and progress towards the realization of quality inclusive education for all

The Extracellular Matrix Component Psl Provides Fast-Acting Antibiotic Defense in Pseudomonas aeruginosa Biofilms

Bacteria within biofilms secrete and surround themselves with an extracellular matrix, which serves as a first line of defense against antibiotic attack. Polysaccharides constitute major elements of the biofilm matrix and are implied in surface adhesion and biofilm organization, but their contributions to the resistance properties of biofilms remain largely elusive. Using a combination of static and continuous-flow biofilm experiments we show that Psl, one major polysaccharide in the Pseudomonas aeruginosa biofilm matrix, provides a generic first line of defense toward antibiotics with diverse biochemical properties during the initial stages of biofilm development. Furthermore, we show with mixed-strain experiments that antibiotic-sensitive “non-producing” cells lacking Psl can gain tolerance by integrating into Psl-containing biofilms. However, non-producers dilute the protective capacity of the matrix and hence, excessive incorporation can result in the collapse of resistance of the entire community. Our data also reveal that Psl mediated protection is extendible to E. coli and S. aureus in co-culture biofilms. Together, our study shows that Psl represents a critical first bottleneck to the antibiotic attack of a biofilm community early in biofilm development.National Institutes of Health (U.S.). National Institute of Environmental Health Sciences (Training Grant in Toxicology 5 T32 ES7020-37

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome