Gut microbiome features are associated with sepsis onset and outcomes

Background: Epidemiologic studies have linked antibiotic exposure to subsequent sepsis, suggesting that microbiome disruption may be in the causal pathway and an independent risk factor. This study tests whether variation in the gut microbiota associates with risk of sepsis onset and its outcomes. Methods: Using a validated surveillance definition, patients with an archived rectal swab from intensive care and hematology units were screened for sepsis. After confirmation by chart review, cases were matched to controls in a 1:2 ratio based on age, gender, and collection date. Relative taxon abundance was measured by sequence analysis of 16S rRNA gene amplicons; total bacterial abundance was measured by qPCR of the 23S rRNA gene. Conditional logistic regression identified clinical and microbiota variables associated with sepsis. Results: There were 103 sepsis cases matched to 206 controls. In a final model adjusting for exposure to broad-spectrum antibiotics and indwelling vascular catheters, high relative abundance (RA) of Enterococcus (Odds Ratio (OR) 1.36 per 10% increase, P=.016) and high total bacterial abundance (OR 1.50 per 10-fold increase in 23S copies/µL, P =.001) were independently associated with sepsis. Decreased RA of butyrate-producing bacteria also independently associated with sepsis (OR 1.20 for 10% decrease in RA, P =.041), and mortality in unadjusted analysis (OR=1.47 for 10% decrease in RA, P=.034). Conclusions: This study indicates that the microbiota is altered at sepsis onset. The decreased RA of butyrate-producing bacteria in sepsis also associates with mortality, suggesting a therapeutic role for prebiotics and probiotics in the prevention and treatment of sepsis.

Resistome analyses of sputum from COPD and healthy subjects reveals bacterial load-related prevalence of target genes

BackgroundAntibiotic resistance is a major global threat. We hypothesised that the chronic obstructive pulmonary disease (COPD) airway is a reservoir of antimicrobial resistance genes (ARGs) that associate with microbiome-specific COPD subgroups.ObjectiveTo determine the resistance gene profiles in respiratory samples from COPD patients and healthy volunteers.MethodsQuantitative PCR targeting 279 specific ARGs was used to profile the resistomes in sputum from subjects with COPD at stable, exacerbation and recovery visits (n=55; COPD-BEAT study), healthy controls with (n=7) or without (n=22) exposure to antibiotics in the preceding 12 months (EXCEED study) and in bronchial brush samples from COPD (n=8) and healthy controls (n=7) (EvA study).ResultsARG mean (SEM) prevalence was greater in stable COPD samples (35.2 (1.6)) than in healthy controls (27.6 (1.7); p=0.004) and correlated with total bacterial abundance (r2=0.23; p<0.001). Prevalence of ARG positive signals in individuals was not related to COPD symptoms, lung function or their changes at exacerbation. In the COPD subgroups designated High γProteobacteria and High Firmicutes, ARG prevalence was not different at stable state but significantly declined from stable through exacerbation to recovery in the former (p=0.011) without changes in total bacterial abundance. The ARG patterns were similar in COPD versus health, COPD microbiome-subgroups and between sputum and bronchoscopic samples independent of antibiotic exposure in the last 12 months.ConclusionsARGs are highly prevalent in sputum, broadly in proportion to bacterial abundance in both healthy and COPD subjects. Thus, COPD appears to be an ARG reservoir due to high levels of bacterial colonisation.

Bacterioneuston in Lake Baikal: Abundance, Spatial and Temporal Distribution

An aquatic surface microlayer covers more than 70% of the world’s surface. Our knowledge about the biology of the surface microlayer of Lake Baikal, the most ancient lake on Earth with a surface area of 31,500 km2, is still scarce. The total bacterial abundance, the number of cultured heterotrophic temporal bacteria, and the spatial distribution of bacteria in the surface microlayer and underlying waters of Lake Baikal were studied. For the first time, the chemical composition of the surface microlayer of Lake Baikal was determined. There were significant differences and a direct relationship between the total bacterial abundance in the surface microlayer and underlying waters of Lake Baikal, as well as between the number of cultured heterotrophic bacteria in studied water layers in the period of summer stratification. In the surface microlayer, the share of cultured heterotrophic bacteria was higher than in the underlying waters. The surface microlayer was characterized by enrichment with PO43−, total organic carbon and suspended particulate matter compared to underlying waters. A direct relationship was found between the number of bacteria in the surface microlayer and environmental factors, including temperature, total organic carbon and suspended particulate matter concentration.

Structure of microbial communities in phosphorus-limited estuaries along the eastern Adriatic coast

The structure of the microbial food web was studied in six estuary areas along the eastern Adriatic coast during March, July and October 2012. Limitation by phosphorus, not nitrogen, was a common feature for all studied estuaries. Heterotrophic bacteria and autotrophic picoplankton (APP) (particularly picoeukaryotes andSynechococcus) can reach notable abundances and biomasses, suggesting potential importance of the picoplankton community in P-limited estuarine environments. The main features of the microbial community structure in these environments included: (1) higher heterotrophic biomass in comparison to autotrophic biomass within the picoplankton community; (2) general domination of picoeukaryotes within the APP community, and increase of absolute and relative biomass of prokaryotic autotrophs (ProchlorococcusandSynechococcus) in the total APP in P-limited conditions; (3) domination ofSynechococcusoverProchlorococcusbiomass in all studied conditions, and common spatial distribution of these two groups of cyanobacteria, which was mostly determined by concentration of phosphorus; (4) relatively high contribution (about 50%) of LNA bacteria in the total bacterial abundance; and (5) relatively high contribution (about 33%) of heterotrophic pico-flagellates in the total flagellate abundance.

Analysis of Changes in Diversity and Abundance of the Microbial Community in a Cystic Fibrosis Patient over a Multiyear Period

The evolution of pulmonary disease in cystic fibrosis (CF) usually begins when bacteria get trapped in mucus in the lungs and become established as a chronic infection. While most CF patients experience periods of stability, pulmonary exacerbations (PEs) can occur multiple times per year and result in permanent damage to the lungs. Little is known of the shift from a period of stability to a PE, but this shift is likely to be attributed to changes in the bacterial community. Here, we identified changes in the lung microbiota to determine if they reflect patient health, indicate the onset of exacerbations, or are related to antibiotic treatment. In contrast to most bacterial studies on CF, we collected weekly samples from an adult CF patient over a period of 3 years and performed quantitative PCR (qPCR) and Illumina sequencing on those samples. While many DNA-based studies have shown the CF microbiota to be relatively stable, we observed an increase in the total bacterial abundance over time (P< 0.001), while the number of different taxa (bacterial richness) and the number of different taxa and their abundances (diversity) significantly decreased over time (P< 0.03), which was likely due to repeated antibiotic exposure. Using genus-specific primers with qPCR, we observed an increase in the abundance ofBurkholderia multivorans, a CF-associated pathogen, prior to the occurrence of a PE (P= 0.006). Combining these DNA-based techniques with frequent sampling identified a potential initiator for exacerbations and described a response of the CF microbiota to time and antibiotic treatment not observed in previous CF microbiota studies.

Spatial Variation of Bacteria in Surface Waters of Paranaguá and Antonina Bays, Paraná, Brazil

Spatial variability in the concentration of total bacteria, saprophytes and coliforms abundance was investigated in surface waters of Paranaguá and Antonina Bays. Six points along a profile from the entrance of Paranaguá Bay to the innermost part of Antonina Bay, were sampled on February 26, 1997. Temperature, salinity, dissolved oxygen, pH, particulate organic carbon, water transparency and seston were also measured. Determination of total bacterial abundance and biomass were made with the epifluorescent method. Saprophytic bacteria counts were conducted with ZoBell 2216E culture medium with fresh and 32‰ water and the coliform MPN was enumerated with the chromogenic substrate method. Principal component analysis of biotic and abiotic data showed a gradient from the innermost bay to the baymouth bar with an increase in total and halophobic aerobic cultivated bacteria concentration at Antonina Bay. Greatest values of halophilic aerobic cultivated bacteria were found at the bay’s middle part. The greatest fecal coliform number was observed near Paranaguá City. We concluded that regarding bacterial spatial distribution the outer region of the estuary was highly influenced by the adjacent ocean and that the inner part had typical estuarine characteristics.