Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling

Background: The human gut microbiota has been implicated in most aspects of health and disease; however, most of the bacteria in this community are considered unculturable, so studies have relied on molecular-based methods. These methods generally do not permit the isolation of organisms, which is required to fully explore the functional roles of bacteria for definitive association with host phenotypes. Using a combination of culture and 16S rRNA gene sequencing, referred to as culture-enriched molecular profiling, we show that the majority of the bacteria identified by 16S sequencing of the human gut microbiota can be cultured. Methods: Five fresh, anaerobic fecal samples were cultured using 33 media and incubation of plates anaerobically and aerobically resulted in 66 culture conditions for culture-enriched molecular profiling. The cultivable portion of the fecal microbiota was determined by comparing the operational taxonomic units (OTUs) recovered by 16S sequencing of the culture plates to OTUs from culture-independent sequencing of the fecal sample. Targeted isolation of Lachnospiraceae strains using conditions defined by culture-enriched molecular profiling was carried out on two fresh stool samples. Results: We show that culture-enriched molecular profiling, utilizing 66 culture conditions combined with 16S rRNA gene sequencing, allowed for the culturing of an average of 95 % of the OTUs present at greater than 0.1 % abundance in fecal samples. Uncultured OTUs were low abundance in stool. Importantly, comparing culture-enrichment to culture-independent sequencing revealed that the majority of OTUs were detected only by culture, highlighting the advantage of culture for studying the diversity of the gut microbiota. Applying culture-enriched molecular profiling to target Lachnospiraceae strains resulted in the recovery of 79 isolates, 12 of which are on the Human Microbiome Project's "Most Wanted" list. Conclusions: We show that, through culture-enriched molecular profiling, the majority of the bacteria in the human gut microbiota can be cultured and this method revealed greater bacterial diversity compared to culture-independent sequencing. Additionally, this method could be applied for the targeted recovery of a specific bacterial group. This approach allows for the isolation of bacteria of interest from the gut microbiota, providing new opportunities to explore mechanisms of microbiota-host interactions and the diversity of the human microbiota.</p

Recycling of plastic wastes generated from COVID-19: A comprehensive illustration of type and properties of plastics with remedial options

Plastic has contributed enormously to the healthcare sector and towards public health safety during the COVID-19 pandemic. With the frequent usage of plastic-based personal protective equipment (PPEs) (including face masks, gloves, protective body suits, aprons, gowns, face shields, surgical masks, and goggles), by frontline health workers, there has been a tremendous increase in their manufacture and distribution. Different types of plastic polymers are used in the manufacture of this equipment, depending upon their usage. However, since a majority of these plastics are still single-use plastics (SUP), they are not at all eco-friendly and end up generating large quantities of plastic waste. The overview presents the various available and practiced methods in vogue for disposal cum treatment of these highly contaminated plastic wastes. Among the current methods of plastic waste disposal, incineration and land filling are the most common ones, but both these methods have their negative impacts on the environment. Alongside, numerous methods that can be used to sterilize them before any treatment have been discussed. There are several new sorting technologies, to help produce purer polymers that can be made to undergo thermal or chemical treatments. Microbial degradation is one such novel method that is under the spotlight currently and being studied extensively, because of its ecological advantages, cost-effectiveness, ease of use, and maintenance. In addition to the deliberations on the methods, strategies have been enumerated for combination of different methods, vis-a-vis studying the life cycle assessment towards a more circular economy in handling this menace to protect mankind

Development of paleoceanographic proxies based on oxygen isotope analysis of sponge spicule and biomarker

해면 골침에 대한 산소동위원소 분석을 통해 과거의 고해양 프록시를 개발하는 목적에서 수행된 연구임1

Combined inorganic nitrogen sources influence the release of extracellular compounds that drive mutualistic interactions in microalgal‒bacterial co-cultures

Abstract We investigated the role of extracellular metabolites released during mutualistic interactions in co-cultures of a microalga, Tetradesmus obliquus IS2 or Coelastrella sp. IS3, and a bacterium, Variovorax paradoxus IS1, grown with varying levels of NO3–N and NH4–N. Both NO3–N and NH4–N were added to modified Bold’s basal medium at 16:0, 12:4, 8:8; 4:12 and 0:16 molar ratios by keeping a final N:P ratio of 16:1. Monocultures of microalgae grown with nitrate alone showed enhanced growth (&gt; twofold) than ammonium, while the bacterial strain cultured with ammonium alone exhibited a &gt; 1.3-fold increase in growth than nitrate. Co-culturing performed higher growth at combined nitrate and ammonium supply as compared to the single cultures. The same ratio of nitrate and ammonium resulted in superior growth of microalgae (&gt; 1.7-fold) and the bacterium (&gt; 4.1-fold) as compared to the monocultures. Uptake of NO3–N, NH4–N and PO4–P by monocultures or co-cultures depended on the ratio of two inorganic nitrogen sources used. The composition of organic acids, amino acids and simple sugars in exudates from monocultures varied with the ratios of nitrate and ammonium in the medium. Thus, the present novel study demonstrates that the release of exudates is affected both qualitatively and quantitatively during mutualistic interactions in microalgal‒bacterial co-cultures under the impact of inorganic nitrogen sources. Our results suggest that the variables such as inorganic nitrogen sources and extracellular metabolites released need to be considered while using co-cultures for effective bioremediation of wastewaters.</jats:p

Acid-adapted microalgae exhibit phenotypic changes for their survival in acid mine drainage samples

ABSTRACT Phenotypic plasticity or genetic adaptation in an organism provides phenotypic changes when exposed to the extreme environmental conditions. The resultant physiological and metabolic changes greatly enhance the organism's potential for its survival in such harsh environments. In the present novel approach, we tested the hypothesis whether acid-adapted microalgae, initially isolated from non-acidophilic environments, can survive and grow in acid-mine-drainage (AMD) samples. Two acid-adapted microalgal strains, Desmodesmus sp. MAS1 and Heterochlorella sp. MAS3, were tested individually or in combination (co-culture) for phenotypic changes during their growth in samples collected from AMD. The acid-adapted microalgae in AMD exhibited a two-fold increase in growth when compared with those grown at pH 3.5 in BBM up to 48 h and then declined. Furthermore, oxidative stress triggered several alterations such as increased cell size, granularity, and enhanced lipid accumulation in AMD-grown microalgae. Especially, the apparent limitation of phosphate in AMD inhibited the uptake of copper and iron in the cultures. Interestingly, growth of the acid-adapted microalgae in AMD downregulated amino acid metabolic pathways as a survival mechanism. This study demonstrates for the first time that acid-adapted microalgae can survive under extreme environmental conditions as exist in AMD by effecting significant phenotypic changes.</jats:p