Universal abundance fluctuations across microbial communities, tropical forests, and urban populations.

The growth of complex populations, such as microbial communities, forests, and cities, occurs over vastly different spatial and temporal scales. Although research in different fields has developed detailed, system-specific models to understand each individual system, a unified analysis of different complex populations is lacking; such an analysis could deepen our understanding of each system and facilitate cross-pollination of tools and insights across fields. Here, we use a shared framework to analyze time-series data of the human gut microbiome, tropical forest, and urban employment. We demonstrate that a single, three-parameter model of stochastic population dynamics can reproduce the empirical distributions of population abundances and fluctuations in all three datasets. The three parameters characterizing a species measure its mean abundance, deterministic stability, and stochasticity. Our analysis reveals that, despite the vast differences in scale, all three systems occupy a similar region of parameter space when time is measured in generations. In other words, although the fluctuations observed in these systems may appear different, this difference is primarily due to the different physical timescales associated with each system. Further, we show that the distribution of temporal abundance fluctuations is described by just two parameters and derive a two-parameter functional form for abundance fluctuations to improve risk estimation and forecasting.

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes.

Microbiome engineering offers the potential to leverage microbial communities to improve outcomes in human health, agriculture, and climate. To translate this potential into reality, it is crucial to reliably predict community composition and function. But a brute force approach to cataloging community function is hindered by the combinatorial explosion in the number of ways we can combine microbial species. An alternative is to parameterize microbial community outcomes using simplified, mechanistic models, and then extrapolate these models beyond where we have sampled. But these approaches remain data-hungry, as well as requiring an a priori specification of what kinds of mechanisms are included and which are omitted. Here, we resolve both issues by introducing a mechanism-agnostic approach to predicting microbial community compositions and functions using limited data. The critical step is the identification of a sparse representation of the community landscape. We then leverage this sparsity to predict community compositions and functions, drawing from techniques in compressive sensing. We validate this approach on in silico community data, generated from a theoretical model. By sampling just [Formula: see text]1% of all possible communities, we accurately predict community compositions out of sample. We then demonstrate the real-world application of our approach by applying it to four experimental datasets and showing that we can recover interpretable, accurate predictions on composition and community function from highly limited data.

Protein cost minimization promotes the emergence of coenzyme redundancy.

SignificanceMetabolism relies on a small class of molecules (coenzymes) that serve as universal donors and acceptors of key chemical groups and electrons. Although metabolic networks crucially depend on structurally redundant coenzymes [e.g., NAD(H) and NADP(H)] associated with different enzymes, the criteria that led to the emergence of this redundancy remain poorly understood. Our combination of modeling and structural and sequence analysis indicates that coenzyme redundancy may not be essential for metabolism but could rather constitute an evolved strategy promoting efficient usage of enzymes when biochemical reactions are near equilibrium. Our work suggests that early metabolism may have operated with fewer coenzymes and that adaptation for metabolic efficiency may have driven the rise of coenzyme diversity in living systems.

Ecological landscapes guide the assembly of optimal microbial communities.

Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia.

Pinned, locked, pushed, and pulled traveling waves in structured environments.

Traveling fronts describe the transition between two alternative states in a great number of physical and biological systems. Examples include the spread of beneficial mutations, chemical reactions, and the invasions by foreign species. In homogeneous environments, the alternative states are separated by a smooth front moving at a constant velocity. This simple picture can break down in structured environments such as tissues, patchy landscapes, and microfluidic devices. Habitat fragmentation can pin the front at a particular location or lock invasion velocities into specific values. Locked velocities are not sensitive to moderate changes in dispersal or growth and are determined by the spatial and temporal periodicity of the environment. The synchronization with the environment results in discontinuous fronts that propagate as periodic pulses. We characterize the transition from continuous to locked invasions and show that it is controlled by positive density-dependence in dispersal or growth. We also demonstrate that velocity locking is robust to demographic and environmental fluctuations and examine stochastic dynamics and evolution in locked invasions.

Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates.

Chirality in shape and motility can evolve rapidly in microbes and cancer cells. To determine how chirality affects cell fitness, we developed a model of chiral growth in compact aggregates such as microbial colonies and solid tumors. Our model recapitulates previous experimental findings and shows that mutant cells can invade by increasing their chirality or switching their handedness. The invasion results either in a takeover or stable coexistence between the mutant and the ancestor depending on their relative chirality. For large chiralities, the coexistence is accompanied by strong intermixing between the cells, while spatial segregation occurs otherwise. We show that the competition within the aggregate is mediated by bulges in regions where the cells with different chiralities meet. The two-way coupling between aggregate shape and natural selection is described by the chiral Kardar-Parisi-Zhang equation coupled to the Burgers' equation with multiplicative noise. We solve for the key features of this theory to explain the origin of selection on chirality. Overall, our work suggests that chirality could be an important ecological trait that mediates competition, invasion, and spatial structure in cellular populations.

Diversity, distribution and antibiotic resistance of Enterococcus spp. recovered from tomatoes, leaves, water and soil on U.S. Mid-Atlantic farms.

Antibiotic-resistant enterococci are important opportunistic pathogens and have been recovered from retail tomatoes. However, it is unclear where and how tomatoes are contaminated along the farm-to-fork continuum. Specifically, the degree of pre-harvest contamination with enterococci is unknown. We evaluated the prevalence, diversity and antimicrobial susceptibilities of enterococci collected from tomato farms in the Mid-Atlantic United States. Tomatoes, leaves, groundwater, pond water, irrigation ditch water, and soil were sampled and tested for enterococci using standard methods. Antimicrobial susceptibility testing was performed using the Sensititre microbroth dilution system. Enterococcus faecalis isolates were characterized using amplified fragment length polymorphism to assess dispersal potential. Enterococci (n = 307) occurred in all habitats and colonization of tomatoes was common. Seven species were identified: Enterococcus casseliflavus, E. faecalis, Enterococcus gallinarum, Enterococcus faecium, Enterococcus avis, Enterococcus hirae and Enterococcus raffinosus. E. casseliflavus predominated in soil and on tomatoes and leaves, and E. faecalis predominated in pond water. On plants, distance from the ground influenced presence of enterococci. E. faecalis from samples within a farm were more closely related than those from samples between farms. Resistance to rifampicin, quinupristin/dalfopristin, ciprofloxacin and levofloxacin was prevalent. Consumption of raw tomatoes as a potential exposure risk for antibiotic-resistant Enterococcus spp. deserves further attention.

Functional convergence in slow-growing microbial communities arises from thermodynamic constraints.

The dynamics of microbial communities is complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The central element of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accumulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network-independent of species composition and biochemical details-providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial environments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum free energy dissipation. Our results predict the decrease of functional convergence in faster growing communities, which we validate by analyzing experimental data from anaerobic digesters. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.

Whole-genome shotgun sequence of the sulfur-oxidizing chemoautotroph Pseudaminobacter salicylatoxidans KCT001.

The facultatively sulfur-oxidizing chemolithoautotrophic alphaproteobacterium Pseudaminobacter salicylatoxidans KCT001 (MTCC 7265) belongs to the family Phyllobacteriaceae of the order Rhizobiales. Analysis of its genome offers valuable insight into the adaptive specializations and evolution of free-living soil bacteria that are phylogenetically closely related to symbiotic and invasive rhizobacteria.

Occurrence and antibiotic resistance of multiple Salmonella serotypes recovered from water, sediment and soil on mid-Atlantic tomato farms.

Salmonella outbreaks associated with the consumption of raw tomatoes have been prevalent in recent years. However, sources of Salmonella contamination of tomatoes remain poorly understood. The objectives of this study were to identify ecological reservoirs of Salmonella on tomato farms, and to test antimicrobial susceptibilities of recovered Salmonella isolates. Fourteen Mid-Atlantic tomato farms in the U.S. were sampled in 2009 and 2010. Groundwater, irrigation pond water, pond sediment, irrigation ditch water, rhizosphere and irrigation ditch soil, leaves, tomatoes, and swabs of harvest bins and worker sanitary facilities were analyzed for Salmonella using standard culture methods and/or a flow-through immunocapture method. All presumptive Salmonella isolates (n=63) were confirmed using PCR and the Vitek(®) 2 Compact System, and serotyped using the Premi(®)Test Salmonella and a conventional serotyping method. Antimicrobial susceptibility testing was carried out using the Sensititre™ microbroth dilution system. Four of the 14 farms (29%) and 12 out of 1,091 samples (1.1%) were found to harbor Salmonella enterica subsp. enterica. Salmonella was isolated by the immunocapture method from soil, while the culture method recovered isolates from irrigation pond water and sediment, and irrigation ditch water. No Salmonella was detected on leaves or tomatoes. Multiple serotypes were identified from soil and water, four of which-S. Braenderup, S. Javiana, S. Newport and S. Typhimurium-have been previously implicated in Salmonella outbreaks associated with tomato consumption. Resistance to sulfisoxazole was prevalent and some resistance to ampicillin, cefoxitin, amoxicillin/clavulanic acid, and tetracycline was also observed. This study implicates irrigation water and soil as possible reservoirs of Salmonella on tomato farms and irrigation ditches as ephemeral habitats for Salmonella. The findings point to the potential for pre-harvest contamination of tomatoes from contaminated irrigation water or from soil or water splash from irrigation ditches onto low-lying portions of tomato plants.

The evaluation of a PCR-based method for identification of Salmonella enterica serotypes from environmental samples and various food matrices.

The most commonly used method for serotyping Salmonella spp. is based on the Kaufmann-White scheme, and is composed of serological reactions using antibodies to LPS agglutinins. The multiplex PCR used in this investigation was established by Kim et al. to serotype the 30 most common clinical Salmonella serotypes, as determined by CDC. The PCR assay consists of two five-plex reactions and a single two-plex PCR reaction, based on six genetic loci from Salmonella enterica serotype Typhimurium and four loci from S. enterica serotype Typhi. In this investigation, we further evaluated the method for serotyping Salmonella spp. using a reference collection, environmental samples collected from a Mid-Atlantic region tomato farm study, four food matrices spiked with different Salmonella serotypes and a proficiency test. The PCR assay was first evaluated using DNA isolated from pure cultures of isolates obtained from various clinical and environmental samples, and then DNA isolated from broth cultures of food matrices of "Red round" and Roma tomatoes, Romaine lettuce, green onions and Serrano peppers spiked with serotypes Newport, Typhimurium, Javiana and Saintpaul, respectively. The results showed that the PCR assay correctly serotyped Salmonella spp. from the clinical, environmental, spiked food matrices, and proficiency test samples. These findings are significant because the PCR assay was successful in the identification of Salmonella in the spiked samples in a broth culture containing other non-salmonella organism. This method may be a useful resource for the food safety community.

A case of recurrent pneumothoraces in a newborn.

Pneumothoraces are not an uncommon finding in the newborn period. Recurrent pneumothoraces can be associated with complications of prematurity or use of ventilators but can be seen in rapidly progressive cystic lung disease. We report a case of recurrent pneumothoraces in an infant with the rapidly progressive cystic disease in the setting of an absent right pulmonary artery. The patient ultimately underwent pneumonectomy for definitive management of the recurrent unilateral pneumothoraces.

Impact of Living Donor Liver Transplantation on COVID-19 Clinical Outcomes from a Quaternary Care Centre in Delhi.

Background and Aims: The anticipated fear of serious outcomes in coronavirus infected liver transplant recipients led to disruption of transplant services globally. The aim of our study was to analyze COVID-19 severity in transplant recipients and to compare the difference of COVID-19 clinical outcomes in early (<1 year) vs. late (>1 year) post-transplant period. Methods: 41 post-living donor liver transplant recipients with COVID-19 infection were studied retrospectively from 1st April 2020 to 28th February 2021. Results: The median age was 49.00 years with a male preponderance (80.49%). Fifteen patients had infection within 1 year of transplant and 26 were infected after 1 year of transplant. The overall median interval between transplantation and COVID-19 diagnosis was 816.00 days. Fever and malaise were the common presenting symptoms. The most common associated comorbidities were diabetes mellitus (65.85%) and hypertension (46.34%). The severity of illness was mild in 28 (68.29%), moderate in 4 (9.76%), severe in 6 (14.63%) and critical in 3 (7.32%). To identify associated risk factors, we divided our patients into less severe and more severe groups. Except for lymphopenia, there was no worsening of total bilirubin, transaminases, alkaline phosphatase, and gamma-glutamyl transferase in the more severe group. Eight (19.51%) patients required intensive care unit admission and three (7.32%) died, while none suffered graft rejection. In recipients with early vs. late post-transplant COVID-19 infection, there were similar outcomes in terms of severity of COVID-19 illness, intensive care unit care need, requirement of respiratory support, and death. Conclusion: Living donor liver transplantation can be performed during the COVID-19 pandemic without the fear of poor recipient outcome in cases of unfortunate contraction of severe acute respiratory syndrome coronavirus-2.

Whole-genome shotgun sequencing of the sulfur-oxidizing chemoautotroph Tetrathiobacter kashmirensis.

The chemolithoautotrophic betaproteobacterium Tetrathiobacter kashmirensis belongs to the family Alcaligenaceae and is phylogenetically closely related to pathogens such as Taylorella and Bordetella species. While a complete inorganic sulfur oxidation gene cluster, soxCDYZAXWB, is present in its genome, pathogenicity islands or genes associated with virulence, disease, cellular invasion, and/or intracellular resistance are completely absent.

Unexpected decline in pediatric asthma morbidity during the coronavirus pandemic.

The Coronavirus disease 2019 (COVID-19) pandemic profoundly impacted health care utilization. We evaluated asthma-related emergency department (ED) and inpatient health care utilization by a county-specific Medicaid population, ages 2-18, during the COVID-19 pandemic and compared it to utilization from a 3-year average including 2017-2019. All-cause ED utilization and asthma medication fill rates were evaluated during the same timeframes. Relative to the 2017-2019 3-year average, cumulative asthma-related ED visits from January through June decreased by 45.8% (p = .03) and inpatient admission rates decreased by 50.5% (p = .03). The decline in asthma-related ED utilization was greater than the reduction of overall ED use during the same time period, suggesting that the decline involved factors specific to asthma and was not due solely to avoidance of health care facilities. Fill rates for asthma controller medications decreased during this time (p = .03) and quick relief medication fill rates had no significant change (p = .31). Multiple factors may have contributed to the decrease in acute asthma health care visits. Locally, decreased air pollution and viral exposures coincided with the "Stay-at-home" order in Ohio, and increased utilization of telehealth for assessment during exacerbations may have impacted outcomes. Identification of the cause of the decline in visit rates could spur new interventions to limit the need for ED and inpatient visits for asthma patients, leading to both economic and health-associated benefits.

Complementary resource preferences spontaneously emerge in diauxic microbial communities.

Many microbes grow diauxically, utilizing the available resources one at a time rather than simultaneously. The properties of communities of microbes growing diauxically remain poorly understood, largely due to a lack of theory and models of such communities. Here, we develop and study a minimal model of diauxic microbial communities assembling in a serially diluted culture. We find that unlike co-utilizing communities, diauxic community assembly repeatably and spontaneously leads to communities with complementary resource preferences, namely communities where species prefer different resources as their top choice. Simulations and theory explain that the emergence of complementarity is driven by the disproportionate contribution of the top choice resource to the growth of a diauxic species. Additionally, we develop a geometric approach for analyzing serially diluted communities, with or without diauxie, which intuitively explains several additional emergent community properties, such as the apparent lack of species which grow fastest on a resource other than their most preferred resource. Overall, our work provides testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microbes.

Survey of patients with cystic fibrosis and caregivers decisions regarding CFTR modulators.

Cystic fibrosis transmembrane conductance regulator (CFTR) modulators are a novel approach to CF management that has become more readily available chronic CF therapies for certain populations of patients with CF. A cross-sectional survey of adults with CF and caregivers of pediatric patients with CF was done in two CF Centers to better understand the decision-making process including the potential influence of social media, CF care-teams, and family members on their decision whether to begin a CFTR modulator. For the 90 participants, the most common influences in the decision to start modulator therapy were the CF providers/care teams (n = 63), parents (n = 49), and individuals with CF (n = 27). The most impactful influence in the decision-making process were providers/care team (n = 47) and parents (n = 18). Social media was an influence for only 12 respondents, with an overall positive impact. Information from the CF Foundation was an influence for 12 participants and the main influence for six participants. The most common reasons for stopping lumacaftor-ivacaftor were having tezacaftor-ivacaftor as an option (n = 25) and side-effects (n = 15). Family and CF clinicians were the two main influences on the decision to initiate modulator therapy. CF clinicians were seen to be the most influential source. Social media had less influence on the decision-making process than expected despite the wide presence of the CF community online.

A comprehensive review on chemical properties and applications of biopolymers and their composites.

In a world that canopies numerous opportunities to advance towards a green sustainable life, biopolymer development offers a platform that fits into the paradigm of achieving an eco-friendly environment whilst reducing reliance on the scarce fossil fuel elements for the fabrication of day-to-day products. Today's technological improvements have aided biopolymer end-products to escalate to higher purposes and soon may have their performance level in par with the petroleum-based synthetic polymers. The motive of this paper is to shimmer light on some aspects of biopolymers that include its classes, properties, composites and applications. Depending on the type of class on the basis of various categories, many enthralling chemistries of polymer composition can be substantiated. Essential properties can imparted to the ensuing biopolymer by altering its chemical configuration and method of synthesis while also focusing on its functional purpose. Nowadays, biopolymer composites blend qualities of one biopolymer with another to acquire an enhanced component that showcases unique explicit attributes. There are several techniques to process biopolymer composites, of which in-situ, infiltration and electrospinning methods have captured considerable limelight. Biopolymers and its composites have embarked captivating impressions in regions of biomedical, packaging, agricultural and automotive applications. Although their efficacy is yet to reach their fossil fuel counterparts, biopolymers have laid a distinguishing mark that will continue to inspire creation of novel substances for many years to come.

Ex situ liver resection and autotransplantation for advanced cholangiocarcinoma.

Advanced cholangiocarcinoma especially those involving the vasculature have extremely limited options of cure. Ex situ liver resection entails performing a total hepatectomy, resecting the tumour on the back-table followed by reimplantation (autotransplantation) of the liver. Application of this technique for these tumours has rarely been done due to complexity of the procedure and the dismal prognosis of the lesions. We present our experience of two cases of advanced intrahepatic cholangiocarcinoma with limited extrahepatic disease who underwent ex situ resection with autotransplantation. They underwent preoperative therapy with a waiting period to assess the tumour biology. Both patients underwent ex situ resection with extended hepatectomy on the back table. Both patients remain well on follow-up 24 months and 20 months, respectively, with excellent quality of life. Despite its technical complexity, ex situ liver resection may offer prolonged overall survival in selected patients with advanced cholangiocarcinoma and limited extrahepatic disease.

Surgical Management of Life Threatening Bleeding after Endoscopic Cystogastrostomy.

Postprocedural bleeding is a rare but life threatening complication of endoscopic cystogastrostomy which may require surgical management in some patients. The presence of adhesions and inflammation due to antecedent acute pancreatitis, difficult location of the bleeding site and breach in the posterior wall of stomach pose significant challenges during the surgical management. Here we have described the surgical approach and technique that we used to manage three patients who required surgery for life threatening bleeding after endoscopic cystogastrostomy.