Bacterial Ecosystem Research Articles

Perinatal microbiota: review of its importance in newborn health.

The use of metagenomics in the study of gut bacterial ecosystems has helped to define a standard, functional genetic profile in newborn infants, so that a bacterial ecosystem will be deemed more "normal" the more similar its functional genetic profile is to a standard. The development of a specific functional enterotype in the first days of life after birth is critical for the priming of the immune system with certain bacterial antigens. Regardless of whether the first gut bacteria are acquired before or just after birth, the newborn microbiota will result from the symbiosis with the environmental microbial flora, especially with the bacterial flora of the mother. The type of delivery, the administration of perinatal antibiotics, the environment, and nutritional exposure, especially breastfeeding, have demonstrated an important relationship with the prevalent gut microbiome.

Nasal Microbiota in RSV Bronchiolitis.

Respiratory Syncytial Virus (RSV) is the leading cause of bronchiolitis, and the severity may be influenced by the bacterial ecosystem. Our aim was to analyze the nasal microbiota from 48 infants affected by bronchiolitis from RSV virus and 28 infants with bronchiolitis but negative for the virus. Results showed a significantly lower biodiversity in the RSV-positive group with respect to the RSV-negative group, a specific microbial profile associated with the RSV-positive group different from that observed in the negative group, and significant modifications in the relative abundance of taxa in the RSV-positive group, as well as in the RSV-A group, with respect to the negative group. Furthermore, microbial network analyses evidenced, in all studied groups, the presence of two predominant sub-networks characterized by peculiar inter- and intra-group correlation patterns as well as a general loss of connectivity among microbes in the RSV-positive group, particularly in the RSV-A group. Our results indicated that infants with more severe bronchiolitis disease, caused by RSV-A infection, present significant perturbations of both the nasal microbiota structure and the microbial relationships. Patients with a milder bronchiolitis course (RSV-B-infected and patients who have cleared the virus) presented less severe alterations.

Organic mulching positively regulates the soil microbial communities and ecosystem functions in tea plantation

BackgroundDifferent mulches have variable effects on soil physicochemical characteristics, bacterial and fungal communities and ecosystem functions. However, the information about soil microbial diversity, community structure and ecosystem function in tea plantation under different mulching patterns was limited. In this study, we investigated bacterial and fungal communities of tea plantation soils under polyethylene film and peanut hull mulching using high-throughput 16S rRNA and ITS rDNA gene Illumina sequencing.ResultsThe results showed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi, and the dominant fungal phyla were Ascomycota, Mortierellomycota and Basidiomycota in all samples, but different mulching patterns affected the distribution of microbial communities. At the phylum level, the relative abundance of Nitrospirae in peanut hull mulching soils (3.24%) was significantly higher than that in polyethylene film mulching soils (1.21%) in bacterial communities, and the relative abundances of Mortierellomycota and Basidiomycota in peanut hull mulching soils (33.72, 21.93%) was significantly higher than that in polyethylene film mulching soils (14.88, 6.53%) in fungal communities. Peanut hull mulching increased the diversity of fungal communities in 0–20 cm soils and the diversity of bacterial communities in 20–40 cm soils. At the microbial functional level, there was an enrichment of bacterial functional features, including amino acid transport and metabolism and energy production and conversion, and there was an enrichment of fungal functional features, including undefined saprotrophs, plant pathogens and soils aprotrophs.ConclusionsUnique distributions of bacterial and fungal communities were observed in soils under organic mulching. Thus, we believe that the organic mulching has a positive regulatory effect on the soil bacterial and fungal communities and ecosystem functions, and so, is more suitable for tea plantation.

Manganese removal efficiencies and bacterial community profiles in non-bioaugmented and in bioaugmented sand filters exposed to different temperatures

Biological sand filtration systems are widely used to remove Manganese (Mn) from groundwater. Different experiences have demonstrated that low environmental temperatures decrease the performance of these systems. In order to overcome this problem, in a previous work, a Pseudomonas sagittaria strain named MOB-181, that showed high Mn(II) oxidation and biofilm formation capacities when grown at low temperatures, was isolated. Here, the impact of summer and winter temperatures on Mn removal efficiencies and on bacterial community profiles of both, non-bioaugmented and MOB-181 bioaugmented sand filters, was analyzed. Under summer conditions, MOB-181 inoculated columns showed the best Mn removal performance, removing Mn from the first day of system operation with an efficiency of 27%; also these columns reached an optimum Mn removal efficiency (95%) earlier than control columns (23 days and 29 days, respectively). Under winter conditions, the 27% efficiency was reached earlier for the inoculated columns than for control columns (20 days and 42 days, respectively); and the maximum efficiency (95%) was also reached faster than for the controls (39 days and 54 days, respectively). Bacterial communities profiles were more influenced by temperature changes than by the bioaugmentation process. This work demonstrated the importance of bioaugmentation with the MOB-181 strain to improve Mn removal, by shortening start-up periods, mainly at lower temperatures. Moreover, the obtained data will improve the knowledge on bacterial communities ecosystem involved in Mn removal at different temperatures and should help in developing novel bioaugmentation strategies for the optimization of biological groundwater treatment plants.

Intestinal Microbiota of Fattening Pigs Offered Non-Fermented and Fermented Liquid Feed with and without the Supplementation of Non-Fermented Coarse Cereals.

Introducing high numbers of lactic acid bacteria into the gastrointestinal tract of pigs via fermented liquid feed (FLF) could have an impact on intestinal bacterial ecosystems. Twenty piglets were allocated into four groups and fed a botanically identical liquid diet that was offered either non-fermented (twice), fully fermented or partially fermented but supplemented with 40% of non-fermented coarse cereals. Microbiota studies were performed on the small and large intestine digesta and faecal samples. A 16S rRNA gene amplification was performed within the hypervariable region V4 and sequenced with the Illumina MiSeq platform. R (version 3.5.2) was used for the statistical analyses. The digesta of the small intestines of pigs fed FLF were dominated by Lactobacillaceae (relative abundance up to 95%). In the colonic contents, the abundance of Lactobacillaceae was significantly higher only in the pigs fed the FLF supplemented with non-fermented coarse cereals. Additionally, the digesta of the small and large intestines as well as in the faeces of the pigs fed the FLF supplemented with non-fermented coarse cereals were significantly enriched for two operational taxonomic units (OTUs) belonging to the genus Lactobacillus and Bifidobacterium. The FLF supplemented with non-fermented coarse cereals had probiotic and prebiotic-like impacts on the intestinal and faecal bacterial composition of pigs.

River bacterial community structure and co-occurrence patterns under the influence of different domestic sewage types

Bacterial communities play a critical role in food webs and the biogeochemical cycles of fundamental elements. However, there remains a substantial gap in our knowledge of the anthropogenic impacts on bacterial co-occurrence patterns and ecosystem functions. In this study, we used Illumina high-throughput sequencing to characterize and compare the diversity, composition, co-occurrence patterns, and functional changes in bacterial communities in the Qingliu River under the influence of different types of domestic sewage. Twelve samples had similar dominant phyla, mainly Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, differing only in the proportions of the microorganisms. However, there was a large difference at the genus level, for example, the relative abundance of the genus Dechloromonas in the school sewage water samples (XXW) was much higher than that in the other samples, the genus Chryseobacterium was the dominant bacteria in the residential sewage water samples (JMW), and there were significant differences between the different samples (P < 0.01). This may indicate that external pollution and environmental induction deeply affect the bacterial community assembly in rivers. Network analysis showed that the river bacterial co-occurrence network has a modular structure (divided into 6 modules), and that the microbial taxonomic units from the same module were involved in the carbon and nitrogen cycle (e.g., the CL500-29 marine group and the genus Pseudomonas) and degradation of organic pollutants and toxic compounds (e.g., the genera Massilia and Exiguobacterium). Functional predictions indicate that the function of ABC transporter was highest in the hospital sewage water samples (YYW), while two-component system was more abundant in the XXW samples. In summary, our research provides a new perspective of community assembly in rivers under the influence of human activity.

Characterizing the Microbiome of the Contracted Breast Capsule Using Next Generation Sequencing.

Recent work suggests that bacterial biofilms play a role in capsular contracture (CC). However, traditional culture techniques provide only a limited understanding of the bacterial communities present within the contracted breast. Next generation sequencing (NGS) represents an evolution of polymerase chain reaction technology that can sequence all DNA present in a given sample. The aim of this study was to utilize NGS to characterize the bacterial microbiome of the capsule in patients with CC following cosmetic breast augmentation. We evaluated 32 consecutive patients with Baker grade III or IV CC following augmentation mammoplasty. Specimens were obtained from all contracted breasts (n = 53) during capsulectomy. Tissue specimens from contracted capsules as well as intraoperative swabs of the breast capsule and implant surfaces were obtained. Samples were sent to MicroGenDX Laboratories (Lubbock, TX) for NGS. Specimens collected from 18 of 32 patients (56%) revealed the presence of microbial DNA. The total number of positive samples was 22 of 53 (42%). Sequencing identified a total of 120 unique bacterial species and 6 unique fungal species. Specimens with microbial DNA yielded a mean [standard deviation] of 8.27 [4.8] microbial species per patient. The most frequently isolated species were Escherichia coli (25% of all isolates), Diaphorobacter nitroreducens (12%), Cutibacterium acnes (12%), Staphylococcus epidermidis (11%), fungal species (7%), and Staphylococcus aureus (6%). NGS enables characterization of the bacterial ecosystem surrounding breast implants in unprecedented detail. This is a critical step towards understanding the role this microbiome plays in the development of CC.

Impact of a Multistrain Probiotic Formulation with High Bifidobacterial Content on the Fecal Bacterial Community and Short-Chain Fatty Acid Levels of Healthy Adults.

The consumption of probiotic products is continually increasing, supported by growing scientific evidence of their efficacy. Considering that probiotics may primarily affect health (either positively or negatively) through gut microbiota modulation, the first aspect that should be evaluated is their impact on the intestinal microbial ecosystem. In this study, we longitudinally analyzed the bacterial taxonomic composition and organic acid levels in four fecal samples collected over the course of four weeks from 19 healthy adults who ingested one capsule a day for two weeks of a formulation containing at least 70 billion colony-forming units, consisting of 25% lactobacilli and 75% Bifidobacterium animalis subsp. lactis. We found that 16S rRNA gene profiling showed that probiotic intake only induced an increase in a single operational taxonomic unit ascribed to B. animalis, plausibly corresponding to the ingested bifidobacterial strain. Furthermore, liquid chromatography/mass spectrometry revealed a significant increase in the lactate and acetate/butyrate ratio and a trend toward a decrease in succinate following probiotic administration. The presented results indicate that the investigated probiotic formulation did not alter the intestinal bacterial ecosystem of healthy adults and suggest its potential ability to promote colonization resistance in the gut through a transient increase in fecal bifidobacteria, lactic acid, and the acetate/butyrate ratio.

Antithetic population response to antibiotics in a polybacterial community.

Much is known about the effects of antibiotics on isolated bacterial species, but their influence on polybacterial communities is less understood. Here, we study the joint response of a mixed community of nonresistant Bacillus subtilis and Escherichia coli bacteria to moderate concentrations of the β-lactam antibiotic ampicillin. We show that when the two organisms coexist, their population response to the antibiotic is opposite to that in isolation: Whereas in monoculture B. subtilis is tolerant and E. coli is sensitive to ampicillin, in coculture it is E. coli who can proliferate in the presence of the antibiotic, while B. subtilis cannot. This antithetic behavior is predicted by a mathematical model constrained only by the responses of the two species in isolation. Our results thus show that the collective response of mixed bacterial ecosystems to antibiotics can run counter to what single-species potency studies tell us about their efficacy.

Science of cooking Week 9: Make friends with microbes

Encourage the growth of a special bacterial ecosystem and you have a tasty way to preserve vegetables, says Sam Wong

Turning the “Phage” on Malnutrition and Stunting

Bacteriophages shape bacterial ecosystems, including community membership and their metabolic function. In this issue of Cell Host & Microbe, Mirzaei etal. (2020) identify harbored bacteriophages among a Proteobacteria-dominant community unique to toddlers with stunted growth from Bangladesh, and that confer the capacity to similarly tailor microbiota profiles invitro.

Intestinal microbiota modulation in juvenile Pacú (Piaractus mesopotamicus) by supplementation with Pyropia columbina and β-carotene

The aim was to evaluate the effects of diet supplementation with red seaweed Pyropia columbina or β-carotene on the intestinal microbiota of juvenile Pacu (Piaractus mesopotamicus). Three hundred and fifteen fish (body weight 12.4 ± 2.8 g) were stocked in nine 300-L tanks with 35 fishes per tank and fed for 62 days with a basal feed (BG) or the same feed added with P. columbina (35 g kg−1) (AG) or supplemented with β-carotene (225 g kg−1) (β-CG). From fecal samples of three fishes slaughtered per group at 20th, 41th, and 62th days, plate counts of bacterial populations (enterobacteria, lactic acid bacteria—LAB, total aerobes, and psychrotrophs) and DGGE were made. Enterobacteria counts were lower in AG-group than the other groups throughout the experience (p = 0.016). LAB/enterobacteria ratio was greater in fishes supplemented with AG on 20th day, showing a greater amount of beneficial bacteria than non-beneficial ones. DGGE profiles resulting from the microbiota of β-CG at 62th day were clustered and separated from the rest of the profiles with a difference of 91%. Margalef richness (p = 0.049) and Shannon diversity index (p = 0.044) were lower in β-CG than in AG at 62th day. Taxonomic characterization showed the presence of three phylum: Bacteroidetes, Firmicutes, and Fusobacteria. This is the first study in which the microbiota of juvenile Pacu fed with biofunctional diets was evaluated. Future interventions that modify the bacterial ecosystem could improve the productive performance and ensure the safety of the pacu meat intended for consumption.

Research progress on interactions between Candida albicans and common oral pathogens

Increasing numbers of microbiome studies have enabled the development of a greater understanding of how antagonistic and synergetic microbial interactions influence disease outcomes. Candida albicans is an opportunistic pathogen that is commonly found in human oral microflora. In a healthy oral environment, Candida albicans may potentially but sig-nificantly influence the balance between the oral bacterial ecosystem and the host, leading tooral diseases. The aim of this study is to review the correlation between Candida albicans and oral pathogens and provide a deeper understanding of the nature of oral infec-tious diseases.

Gut microbiota of the scimitar-horned oryx, Oryx dammah

Our aim was to obtain details of the condition of the scimitar-horned oryx (Oryx dammah) and to elucidate the gut microbial diversity of captive individuals of this species. For the first time, 16S rRNA barcoding was used to characterise the faecal microbiota of five captive scimitar-horned oryx individuals. A total of 15 prokaryotic phyla were identified in the five samples. Including Firmicutes (53.40-72.01 %), Bacteroidetes (12.94-23.72 %) and Proteobacteria (1.03-31.74 %), accounting for > 96 % of all the sequences. At the family level, there were < 3.5 % unclassified sequences. In conclusion, these data revealed similarities and differences in gut microbial diversity across the scimitar-horned oryx individuals. These observations advance the current understanding of the bacterial ecosystems in these endangered animals under captivity.

CBMT-40. THE RELATIONSHIP BETWEEN GLIOMA AND THE GUT-BRAIN AXIS

Abstract Recent studies demonstrate the potential role of the microbiome in immune-oncology, revealing specific microbial taxa can augment the effects of various therapeutic modalities against tumors. Gut dysbiosis, a disequilibrium in the host’s bacterial ecosystem, can potentially lead to overrepresentation of some bacteria and favor chronic inflammation and immunosuppression. However, the effects of microbial dysbiosis on non-gastrointestinal cancers in particular gliomas are unknown. Here, we explored the effects of glioma and Temozolomide (TMZ) on the fecal microbiome (FM) in mice (n=24) and FM and metabolome in humans (n=40). Aged C57/B6 mice were implanted with Gl261 tumor cells or vehicle and were assigned to one of the following treatment (oral) groups: vehicle, 5mg/kg TMZ or 25mg/kg TMZ beginning 14 days after surgery for 3-weeks following a 5 day on/2 day off treatment. Fecal samples were collected prior to surgery, at treatment initiation and weekly thereafter until sacrifice and sequenced for 16s RNA. Fecal samples were collected from humans with newly diagnosed glioma before resection, chemoradiation, and after chemoradiation (16s RNA, metabolomic, neurotransmitter analysis). In mice, FM beta diversity was significantly altered with glioma (p=0.003) while the alpha diversity remained unchanged. At a genus and family level analysis the relative abundance of Bacteroides (p=0.01) and Bacteroidaceae (p=0.02) was increased. Beta diversity of mice receiving 5mg/kg TMZ changed from baseline (p=0.02). Collectively, this suggests that glioma alters the FM, to what consequence remains to be explored. Alpha (Observed OTUs, p=0.029) and beta diversity (p=0.034) differences in mice correlated with survival (&lt; 25 - &gt;25 days). In humans, norepinephrine and 5-hydroxyindoleacetic acid were significantly lower in glioma patients at diagnosis compared to controls. Our findings demonstrate for the first time the relationship between glioma and the gut-brain axis. Understanding alterations in the FM in glioma patients may allow novel interventions and should be further investigated.

Mixing effect of polylactic acid microplastic and straw residue on soil property and ecological function.

Microplastics have become a contaminant of increasing concern in soils. Although biodegradable plastics were considered as alternatives of traditional plastics, some evidence showed that biodegradable plastics might produce more microplastics. Until now, the effect of biodegradable microplastics on soil functions and processes, as well as microbial communities is uncertain. Based on high throughput sequencing, enzymatic activity assay and dynamic analysis of soil carbon and nitrogen, we investigated the effects of biodegradable polylactic acid microplastics (PLA MPs) on soil microbiota and related ecological processes under conditions of high or low carbon content. The results showed that PLA MPs had no significant effect on the overall diversity and composition of bacterial communities or related ecosystem functions and processes. However, co-occurrence network analysis revealed that PLA MPs impacted the interactions between constituent species, which might have legacy effect on soil bacterial communities and functions. Our data also revealed that PLA MPs could trade off the priming effect of carbon source. Our results provided an integrated picture in understanding the effects of PLA MPs on soil microbes, properties and ecological functions, which will help to further understand the effects of MPs on terrestrial ecosystems.

Insights into microbial community structure and diversity in oil palm waste compost.

Empty fruit bunch (EFB) and palm oil mill effluent (POME) are the major wastes generated by the oil palm industry in Malaysia. The practice of EFB and POME digester sludge co-composting has shown positive results, both in mitigating otherwise environmentally damaging waste streams and producing a useful product (compost) from these streams. In this study, the bacterial ecosystems of 12-week-old EFB-POME co-compost and POME biogas sludge from Felda Maokil, Johor were analysed using 16S metagenome sequencing. Over ten phyla were detected, with Chloroflexi being the predominant phylum, representing approximately 53% of compost and 23% of the POME microbiome reads. The main bacterial lineage found in the compost and POME was Anaerolinaceae (Chloroflexi) with 30% and 18% of the total gene fragments, respectively. The significant differences between compost and POME communities were abundances of Syntrophobacter, Sulfuricurvum and Coprococcus. No methanogens were identified due to the bias in general 16S primers to eubacteria. The preponderance of anaerobic species in the compost and high abundance of secondary metabolite fermenting bacteria is due to an extended composting time, with anaerobic collapse of the pile due to the tropical heat. Predictive functional profiles of the metagenomes using 16S rRNA marker genes suggest that the presence of enzymes involved in degradation of polysaccharides such as glucoamylase, endoglucanase and arabinofuranosidase, all of which were strongly active in POME. Eubacterial species associated with cellulytic methanogenesis were present in both samples.

Variability in cyanobacteria sensitivity to antibiotics and implications for environmental risk assessment

Once released into the environment antibiotics can kill or inhibit the growth of bacteria, and in turn potentially have effects on bacterial community structure and ecosystem function. Environmental risk assessment (ERA) seeks to establish protection limits to minimise chemical impacts on the environment, but recent evidence suggests that the current regulatory approaches for ERA for antibiotics may not be adequate for protecting bacteria that have fundamental roles in ecosystem function. In this study we assess the differences in interspecies sensitivity of eight species of cyanobacteria to seven antibiotics (cefazolin, cefotaxime, ampicillin, sufamethazine, sulfadiazine, azithromycin and erythromycin) with three different modes of action. We found that variability in the sensitivity to these antibiotics between species was dependent on the mode of action and varied by up to 70 times for β-lactams. Probabilistic analysis using species sensitivity distributions suggest that the current predicted no effect concentration PNEC for the antibiotics may be either over or under protective of cyanobacteria dependent on the species on which it is based and the mode of action of the antibiotic; the PNECs derived for the macrolide antibiotics were over protective but PNECs for β-lactams were generally under protective. For some geographical locations we identify a significant risk to cyanobacteria populations based upon measured environmental concentrations of selected antibiotics. We conclude that protection limits, as determined according to current regulatory guidance, may not always be protective and might be better derived using SSDs and that including toxicity data for a wider range of (cyano-) bacteria would improve confidence for the ERA of antibiotics.

Impact of Selected Cosmetic Ingredients on Common Microorganisms of Healthy Human Skin

Human skin is a complex ecosystem and is host to a large number of microorganisms. When the bacterial ecosystem is balanced and differentiated, skin remains healthy. However, the use of cosmetics can change this balance and promote the appearance of skin diseases. The skin’s microorganisms can utilize some cosmetic components, which either promote their growth, or produce metabolites that influence the skin environment. In this study, we tested the ability of the Malassezia species and some bacterial strains to assimilate substances frequently used in dermal formulations. The growth capability of microorganisms was determined and their lipase activity was analyzed. The growth of all Malassezia spp. in the presence of free acids, free acid esters, and fatty alcohols with a fatty chain length above 12 carbon atoms was observed. No growth was observed in the presence of fatty alcohol ethers, secondary fatty alcohols, paraffin- and silicon-based substances, polymers, polyethylene glycols, quaternary ammonium salts, hydroxy fatty acid esters, or fatty acids and fatty acid esters with a fatty chain length shorter than 12 carbon atoms. The hydrolysis of esters by Malassezia lipases was detected using High Performance Thin Layer Chromatography (HPTLC). The production of free fatty acids as well as fatty alcohols was observed. The growth promotion or inhibition of bacterial strains was only found in the presence of a few ingredients. Based on these results, formulations containing microbiome inert ingredients were developed.

The Gut Microbiome: A New Player in Breast Cancer Metastasis.

There is increasing interest in the role of the gut microbiome in health and disease, and a number of observational and in vitro studies have suggested it may play a role in breast cancer development and progression. Buchta Rosean and colleagues present the first functional evidence that a preexisting disturbance in the gut microbiome leads to increased breast cancer cell metastasis in a mouse model. This discovery places the gut microbiome as a new player in breast cancer metastasis; however, further studies are required to determine the relevance of the findings in this mouse model to human disease. A better understanding of the relationship between the bacterial ecosystem of the gut and progression of breast cancer has enormous potential for improving treatment outcomes for patients with breast cancer.See related article by Buchta Rosean et al., p. 3662.