Quantifying the contribution of microbial immigration in engineered water systems.

Abstract:

:Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this process to the microbial diversity and function in the receiving ecosystems. Currently used methods, i.e., counting shared microbial species, microbial source tracking, and neutral community model, rely on abundance profile to reveal the extent of overlapping between the upstream and downstream communities. Thus, they cannot suggest the quantitative contribution of immigrants to the downstream community function because activities of individual immigrants are not considered after entering the receiving environment. This limitation can be overcome by using an approach that couples a mass balance model with high-throughput DNA sequencing, i.e., ecogenomics-based mass balance. It calculates the net growth rate of individual microbial immigrants and partitions the entire community into active populations that contribute to the community function and inactive ones that carry minimal function. Linking activities of immigrants to their abundance further provides quantification of the contribution from an upstream environment to the downstream community. Considering only active populations can improve the accuracy of identifying key environmental parameters dictating process performance using methods such as machine learning.

journal_name

Microbiome

journal_title

Microbiome

authors

Mei R,Liu WT

doi

10.1186/s40168-019-0760-0

subject

Has Abstract

pub_date

2019-11-06 00:00:00

pages

144

issue

1

issn

2049-2618

pii

10.1186/s40168-019-0760-0

journal_volume

7

pub_type

杂志文章,评审
  • Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.

    abstract:BACKGROUND:The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe inter...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0689-3

    authors: Heinken A,Ravcheev DA,Baldini F,Heirendt L,Fleming RMT,Thiele I

    更新日期:2019-05-15 00:00:00

  • Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore.

    abstract:BACKGROUND:Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly c...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0430-7

    authors: Gobet A,Mest L,Perennou M,Dittami SM,Caralp C,Coulombet C,Huchette S,Roussel S,Michel G,Leblanc C

    更新日期:2018-03-27 00:00:00

  • A comparison of methods used to unveil the genetic and metabolic pool in the built environment.

    abstract:BACKGROUND:A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribo...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0453-0

    authors: Gomez-Silvan C,Leung MHY,Grue KA,Kaur R,Tong X,Lee PKH,Andersen GL

    更新日期:2018-04-16 00:00:00

  • CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

    abstract:BACKGROUND:Culture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between species. RESULTS:Based on 2,900 sequenced reference genomes, we show that 16S rRNA gene copy number (GC...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/2049-2618-2-11

    authors: Angly FE,Dennis PG,Skarshewski A,Vanwonterghem I,Hugenholtz P,Tyson GW

    更新日期:2014-04-07 00:00:00

  • Optimal screening and donor management in a public stool bank.

    abstract:BACKGROUND:Fecal microbiota transplantation is an effective treatment for recurrent Clostridium difficile infection and is being investigated as a treatment for other microbiota-associated diseases. To facilitate these activities, an international public stool bank has been created, which screens donors and processes s...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-015-0140-3

    authors: Kazerouni A,Burgess J,Burns LJ,Wein LM

    更新日期:2015-12-17 00:00:00

  • Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment.

    abstract:BACKGROUND:Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic co...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0255-9

    authors: Wurzbacher C,Fuchs A,Attermeyer K,Frindte K,Grossart HP,Hupfer M,Casper P,Monaghan MT

    更新日期:2017-04-08 00:00:00

  • Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants.

    abstract:BACKGROUND:Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous micr...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-020-00874-1

    authors: Leung MHY,Tong X,Bastien P,Guinot F,Tenenhaus A,Appenzeller BMR,Betts RJ,Mezzache S,Li J,Bourokba N,Breton L,Clavaud C,Lee PKH

    更新日期:2020-06-26 00:00:00

  • The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media.

    abstract:BACKGROUND:Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indigenous populations is required to advance treatment and reduce prevalence. We conducted a systematic ...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0577-2

    authors: Coleman A,Wood A,Bialasiewicz S,Ware RS,Marsh RL,Cervin A

    更新日期:2018-11-05 00:00:00

  • Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments.

    abstract:BACKGROUND:Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of Califo...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0322-2

    authors: Dombrowski N,Seitz KW,Teske AP,Baker BJ

    更新日期:2017-08-23 00:00:00

  • Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences.

    abstract:BACKGROUND:The study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that dete...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-015-0128-z

    authors: Miletto M,Lindow SE

    更新日期:2015-12-10 00:00:00

  • A two-stage microbial association mapping framework with advanced FDR control.

    abstract:BACKGROUND:In microbiome studies, it is important to detect taxa which are associated with pathological outcomes at the lowest definable taxonomic rank, such as genus or species. Traditionally, taxa at the target rank are tested for individual association, followed by the Benjamini-Hochberg (BH) procedure to control fo...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0517-1

    authors: Hu J,Koh H,He L,Liu M,Blaser MJ,Li H

    更新日期:2018-07-25 00:00:00

  • Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.

    abstract:BACKGROUND:Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the rec...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0270-x

    authors: Lee STM,Kahn SA,Delmont TO,Shaiber A,Esen ÖC,Hubert NA,Morrison HG,Antonopoulos DA,Rubin DT,Eren AM

    更新日期:2017-05-04 00:00:00

  • Wild bees and their nests host Paenibacillus bacteria with functional potential of avail.

    abstract:BACKGROUND:In previous studies, the gram-positive firmicute genus Paenibacillus was found with significant abundances in nests of wild solitary bees. Paenibacillus larvae is well-known for beekeepers as a severe pathogen causing the fatal honey bee disease American foulbrood, and other members of the genus are either s...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0614-1

    authors: Keller A,Brandel A,Becker MC,Balles R,Abdelmohsen UR,Ankenbrand MJ,Sickel W

    更新日期:2018-12-22 00:00:00

  • Microbe observation and cultivation array (MOCA) for cultivating and analyzing environmental microbiota.

    abstract:BACKGROUND:The use of culture-independent nucleic acid techniques, such as ribosomal RNA gene cloning library analysis, has unveiled the tremendous microbial diversity that exists in natural environments. In sharp contrast to this great achievement is the current difficulty in cultivating the majority of bacterial spec...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/2049-2618-1-4

    authors: Gao W,Navarroli D,Naimark J,Zhang W,Chao SH,Meldrum DR

    更新日期:2013-01-09 00:00:00

  • Organophosphorus pesticide chlorpyrifos intake promotes obesity and insulin resistance through impacting gut and gut microbiota.

    abstract:BACKGROUND:Disruption of the gut microbiota homeostasis may induce low-grade inflammation leading to obesity-associated diseases. A major protective mechanism is to use the multi-layered mucus structures to keep a safe distance between gut epithelial cells and microbiota. To investigate whether pesticides would induce ...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0635-4

    authors: Liang Y,Zhan J,Liu D,Luo M,Han J,Liu X,Liu C,Cheng Z,Zhou Z,Wang P

    更新日期:2019-02-11 00:00:00

  • Transplanted human fecal microbiota enhanced Guillain Barré syndrome autoantibody responses after Campylobacter jejuni infection in C57BL/6 mice.

    abstract:BACKGROUND:Campylobacter jejuni is the leading antecedent infection to the autoimmune neuropathy Guillain-Barré syndrome (GBS), which is accompanied by an autoimmune anti-ganglioside antibody attack on peripheral nerves. Previously, we showed that contrasting immune responses mediate C. jejuni induced colitis and autoi...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0284-4

    authors: Brooks PT,Brakel KA,Bell JA,Bejcek CE,Gilpin T,Brudvig JM,Mansfield LS

    更新日期:2017-08-08 00:00:00

  • VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition.

    abstract:BACKGROUND:Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epide...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-020-00934-6

    authors: France MT,Ma B,Gajer P,Brown S,Humphrys MS,Holm JB,Waetjen LE,Brotman RM,Ravel J

    更新日期:2020-11-23 00:00:00

  • Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

    abstract:BACKGROUND:Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a ver...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0233-2

    authors: Huson DH,Tappu R,Bazinet AL,Xie C,Cummings MP,Nieselt K,Williams R

    更新日期:2017-01-25 00:00:00

  • Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence.

    abstract:BACKGROUND:High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The obje...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0403-x

    authors: Liu J,Abdelfattah A,Norelli J,Burchard E,Schena L,Droby S,Wisniewski M

    更新日期:2018-01-27 00:00:00

  • Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants.

    abstract:BACKGROUND:Recent evidence supports that the maternal gut microbiota impacts the initial infant gut microbiota. Since the gut microbiota may play a causal role in the development of obesity, it is important to understand how pre-pregnancy weight and gestational weight gain (GWG) impact the gut microbiota of mothers at ...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0332-0

    authors: Stanislawski MA,Dabelea D,Wagner BD,Sontag MK,Lozupone CA,Eggesbø M

    更新日期:2017-09-04 00:00:00

  • Re-evaluating the relationship between missing heritability and the microbiome.

    abstract::Human genome-wide association studies (GWASs) have recurrently estimated lower heritability estimates than familial studies. Many explanations have been suggested to explain these lower estimates, including that a substantial proportion of genetic variation and gene-by-environment interactions are unmeasured in typica...

    journal_title:Microbiome

    pub_type: 信件

    doi:10.1186/s40168-020-00839-4

    authors: Douglas GM,Bielawski JP,Langille MGI

    更新日期:2020-06-08 00:00:00

  • Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China.

    abstract:BACKGROUND:The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulatin...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0572-7

    authors: Liu YR,Delgado-Baquerizo M,Bi L,Zhu J,He JZ

    更新日期:2018-10-18 00:00:00

  • Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms.

    abstract:BACKGROUND:The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0743-1

    authors: Rausch P,Rühlemann M,Hermes BM,Doms S,Dagan T,Dierking K,Domin H,Fraune S,von Frieling J,Hentschel U,Heinsen FA,Höppner M,Jahn MT,Jaspers C,Kissoyan KAB,Langfeldt D,Rehman A,Reusch TBH,Roeder T,Schmitz RA,Schulenb

    更新日期:2019-09-14 00:00:00

  • Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome.

    abstract:BACKGROUND:Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into nat...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-020-00982-y

    authors: Wicaksono WA,Kusstatscher P,Erschen S,Reisenhofer-Graber T,Grube M,Cernava T,Berg G

    更新日期:2021-01-27 00:00:00

  • Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons.

    abstract:BACKGROUND:The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of an...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0228-z

    authors: Miller EA,Livermore JA,Alberts SC,Tung J,Archie EA

    更新日期:2017-01-19 00:00:00

  • Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission.

    abstract:BACKGROUND:The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk. RESULTS:The composition of bifidobacterial c...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0282-6

    authors: Duranti S,Lugli GA,Mancabelli L,Armanini F,Turroni F,James K,Ferretti P,Gorfer V,Ferrario C,Milani C,Mangifesta M,Anzalone R,Zolfo M,Viappiani A,Pasolli E,Bariletti I,Canto R,Clementi R,Cologna M,Crifò T,Cusumano

    更新日期:2017-06-26 00:00:00

  • Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children.

    abstract:BACKGROUND:The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known abou...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-016-0170-5

    authors: Pérez-Losada M,Crandall KA,Freishtat RJ

    更新日期:2016-06-16 00:00:00

  • Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease.

    abstract:BACKGROUND:Whole-genome "shotgun" (WGS) metagenomic sequencing is an increasingly widely used tool for analyzing the metagenomic content of microbiome samples. While WGS data contains gene-level information, it can be challenging to analyze the millions of microbial genes which are typically found in microbiome experim...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0722-6

    authors: Minot SS,Willis AD

    更新日期:2019-08-01 00:00:00

  • Host genetic variation in mucosal immunity pathways influences the upper airway microbiome.

    abstract:BACKGROUND:The degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here, we performed a genetic mapping study of the microbiome in two accessible upper airway sites, the nasopharynx and the nasal vestibule, during two seasons in 144 adult members of a founder po...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-016-0227-5

    authors: Igartua C,Davenport ER,Gilad Y,Nicolae DL,Pinto J,Ober C

    更新日期:2017-02-01 00:00:00

  • Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment.

    abstract:BACKGROUND:Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 t...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-020-00960-4

    authors: Minich JJ,Ali F,Marotz C,Belda-Ferre P,Chiang L,Shaffer JP,Carpenter CS,McDonald D,Gilbert J,Allard SM,Allen EE,Knight R,Sweeney DA,Swafford AD

    更新日期:2021-01-22 00:00:00